2025-08-04 09:36:56 -0700 Updated version number
VERSION
config.site.rosalind.prd
config.site.rosalind.tst

2025-08-04 09:36:40 -0700 For --tpm option, printing both raw and normalized counts
src/gcount.c

2025-08-02 08:17:21 -0700 Added a missing end brace
src/gcount.c

2025-08-01 20:12:53 -0700 Moved code for checking whether to build a localdb
util/gmap_build.pl.in

2025-08-01 11:31:58 -0700 In Transcript_remap_endpoint_coords, fixed check for final exoni
src/transcript-remap.c

2025-08-01 11:30:02 -0700 In Path_solve_junctions, if a solution is not found, advancing pointers to avoid an infinite loop
src/path-solve.c

2025-08-01 11:29:30 -0700 Allowing fp to be NULL
src/outbuffer.c

2025-08-01 11:29:10 -0700 Added mode, now default, for not allowing alignments to extend past the end of the target
src/gexact.c

2025-08-01 11:28:34 -0700 Added assertions
src/genomebits_mismatches.c

2025-08-01 11:28:27 -0700 Added assertions
src/genomebits_indel.c

2025-08-01 11:28:05 -0700 Performing EM for bulk RNA-seq, using multimappers.  Added --tpm flag for normalizing counts
src/gcount.c

2025-08-01 11:26:58 -0700 Added file gen-equiv-class to gcount
src/Makefile.dna.am
src/gen-equiv-class.c
src/gen-equiv-class.h

2025-08-01 11:26:25 -0700 Added function Samread_chr
src/samread.c
src/samread.h

2025-08-01 11:26:03 -0700 Initializing value of ignore_found_score
src/pathpair-eval.c

2025-08-01 11:25:47 -0700 Initializing value of ignore_found_score
src/path-eval.c

2025-08-01 11:23:07 -0700 Fixed buffer overflow in input_oneline by changing reducing fgets by 1 character.  Restructured handling of chastity so compiler does not give a warning
src/shortread.c
src/shortread.h

2025-06-17 16:21:34 -0700 Fixed typo in macro
src/trpath-eval.h

2025-06-17 16:21:20 -0700 Made Path_endpoints_acceptable_p and Trpath_endpoints_acceptable_p check for an alignment match
src/path.c
src/trpath-solve.c

2025-06-17 16:18:50 -0700 Made novel_splicesites work when builtin_ctz is not present
src/genome_sites.c

2025-05-29 15:30:59 -0700 Removed tag for Id
src/altsplice.c
src/trpath-convert.c

2025-05-29 15:30:33 -0700 In Path_trim_qstart_n and Path_trim_qend_n, accounting for ninserts
src/path-trim.c

2025-05-29 15:29:54 -0700 In Path_eval_and_sort, handling the case where all paths are trimmed by chrbounds
src/path-eval.c

2025-05-28 11:38:35 -0700 Updated for latest version
share/index.html

2025-05-28 11:37:45 -0700 Allowing the printing of sequences from a map file without expecting input from stdin
src/get-genome.c

2025-05-28 11:37:08 -0700 In Path_trim_chrbounds, returning false if all segments are before chromosomal start or after chromosomal end
src/path-trim.c

2025-05-06 13:15:13 -0700 For Path_print_sam_nomapping, computing the mate chrpos using Path_genomiclow_softclipped
src/path-print-sam.c

2025-04-18 12:19:09 -0700 Initial import
src/Makefile.gcount.am

2025-04-18 12:19:00 -0700 Updated version number
VERSION
config.site.rosalind.prd
config.site.rosalind.tst

2025-04-18 12:17:34 -0700 Added a test for staying on the same univdiagonal
src/splice.c

2025-04-18 12:16:24 -0700 In paths5_mates and paths3_mates, checking if mate is on a different chromosome
src/stage1hr-paired.c

2025-04-18 12:15:25 -0700 Removed Id tag
src/path-print-sam.c

2025-04-18 12:15:07 -0700 Including correct version of merge-diagonals for large genomes
src/spliceends.c

2025-04-18 12:14:30 -0700 Using new interface to Path_trim_circular_unalias
src/path-eval.c

2025-04-18 12:14:09 -0700 Using new interface to Path_trim_circular_unalias_pair
src/pathpair-eval.c

2025-04-18 12:13:43 -0700 Added include of path-trim.h
src/pathpair.c

2025-04-18 12:12:08 -0700 Modified unalias_path to recompute nmismatches for segments that straddle the circular origin.  In trim_qstart, undoing the addition of the last ninserts to the endpoint.  Applying revisions from 2024-09-09 and 2024-10-14
src/path-trim.c
src/path-trim.h

2025-04-18 12:07:07 -0700 Revised print_program_usage
src/gcount.c

2025-04-18 12:06:47 -0700 Added instructions for gtf_exons and gff3_exons
configure.ac

2025-04-18 12:06:04 -0700 Revised code for deciding whether to build localdb
util/gmap_build.pl.in

2025-04-18 12:05:50 -0700 Revised code for deciding whether to build localdb
util/gmap_cat.pl.in

2025-04-18 12:05:21 -0700 Added instructions for gtf_exons and gff3_exons
util/Makefile.am

2025-04-18 12:04:57 -0700 Removed file that is generated by automake and configure
util/Makefile.in

2025-04-18 11:50:22 -0700 Initial import
util/gff3_exons.pl.in
util/gtf_exons.pl.in

2025-04-18 11:39:13 -0700 Initial import
bootstrap.gcount

2025-03-27 11:10:22 -0700 Using new interface to Path_trim_chrbounds
src/path-eval.c
src/pathpair-eval.c

2025-03-27 11:09:56 -0700 Path_qstart_resolve and Path_qend_resolve now calling Path_trim_chrbounds instead of Path_eval_nmatches
src/path-solve.c

2025-03-27 11:09:25 -0700 Pathpair_resolve now calling Path_trim_chrbounds instead of Path_eval_nmatches
src/pathpair.c

2025-03-27 11:08:59 -0700 Path_trim_chrbounds now returns found_score, and calls Path_eval_nmatches if path->nmatches < 0
src/path-trim.c
src/path-trim.h

2025-03-26 18:31:46 -0700 Added debugging statements
src/trpath.c

2025-03-26 18:31:31 -0700 Fixed bug in Trpath_solve_from_diagonals with return of an uninitialized value
src/trpath-solve.c

2025-03-26 18:30:46 -0700 Added comments
src/tr-extension-search.c

2025-03-26 18:30:35 -0700 Formatting changes
src/stage1hr-paired.c

2025-03-26 18:28:55 -0700 Removed Id tag
src/hitlistpool.c

2025-03-25 19:08:19 -0700 Added support_tables and revising them with splices.  Implemented --splices-dump option
src/gsnap.c

2025-03-25 19:07:34 -0700 Fixed order of parameters in get_exhaustive
src/localdb-read.c

2025-03-25 19:07:22 -0700 Removed dump_splices_fp as a parameter to Knownsplicing_new
src/knownsplicing.c
src/knownsplicing.h

2025-03-25 19:07:07 -0700 Using new interface to Knownsplicing_new
src/support.c

2025-03-21 17:55:31 -0700 Reporting substitutions, even when checking assertions.  Applied revision from 2024-10-27
src/path-print-alignment.c

2025-03-21 14:39:28 -0700 Putting memory into the standard pool instead of the keep pool.  Starting and resetting to empty allocation instead of an initial chunk.  Applied revision from 2024-10-13
src/pathpool.c

2025-03-21 14:36:12 -0700 Keeping track of separate pools for aligned and keep_aligned.  Added macro DEBUG_FILE.  Applied revisions from 2024-10-13 and 2024-10-14
src/mem.c

2025-03-21 14:32:52 -0700 Putting memory into standard pool instead of keep pool
src/spliceendsgen.c

2025-03-21 14:32:38 -0700 Putting memory into standard pool instead of keep pool.  Starting and ending with empty allocation.  Revising chunksizes.  Applied revision from 2024-10-13
src/vectorpool.c

2025-03-21 14:22:37 -0700 Added debugging statements.  Applied revision from 2024-10-31
src/intersectp-simd.c

2025-03-21 14:20:58 -0700 In get_exhaustive, checking for nstreams exceeding max_nstreams.  Applied revision from 2024-10-20
src/localdb-read.c

2025-03-21 14:20:25 -0700 Added option --align-fraction and using new interface to Inbuffer_new.  Set a default seed.  Applied revisions from 2024-09-18, 2024-09-19, and 2024-09-20
src/gsnap.c

2025-03-21 14:08:53 -0700 Keeping track of inner and outer splices separately.  Fixed double-counting of nreads_correct for multimappers.  Reporting multiple alignments.  Applied revisions from 2024-10-02, 2024-10-04, 2024-10-08, and 2024-10-27
src/compare2truth.c

2025-03-21 14:04:34 -0700 Added options --kmer and --print-stats.  Changed default kmer size from 24 to 27.  Using new interface to Inbuffer_new.  Using new interface to Mem_usage_std_heap_add.  Applied revisions from 2024-09-18, 2024-09-20, 2024-10-12, and 2024-10-31
src/gfilter.c

2025-03-21 13:54:00 -0700 Using new interface to Inbuffer_new.  Using new interface to Mem_usage_std_heap_add.  Applied revisions from 2024-09-18, 2024-09-20, and 2024-10-12
src/gexact.c

2025-03-21 13:52:06 -0700 Using new interface to Inbuffer_new.  Implemented option --align-fraction.  Using new interface to Mem_usage_std_heap_add.  Applied revisions from 2024-09-18, 2024-09-19, and 2024-10-12
src/gmap.c

2025-03-21 13:50:58 -0700 Using new interface to Reader_new and Reader_set_sequence.  Applied revision from 2024-10-10
src/stage1.c

2025-03-21 13:42:45 -0700 Added field skip_prob and implemented determine_skipp.  Inbuffer_new takes seed as a parameter.  Checking part_interval instead of part_modulus.  Applied revisions from 2024-09-18, 2024-09-20, and 2024-10-02
src/inbuffer.c
src/inbuffer.h

2025-03-21 13:38:45 -0700 Added option --atsnps.  Applied revision from 2024-10-31
src/snpindex.c

2025-03-21 13:33:27 -0700 In Path_qstart_resolve and Path_qend_resolving, using Intlist_head_set instead of Intlist_head_incr on path->nmismatches.  Applied revision from 2024-11-04
src/path-solve.c

2025-03-21 13:13:11 -0700 No longer avoiding negative values for pos5 or pos3 given to fill_splicesites.  Rejecting revision from 2024-11-20
src/genome_sites.c

2025-03-21 11:39:43 -0700 Checking for the possibility that pos5 >= pos3.  Avoiding negative values for pos5 or pos3 given to fill_splicesites.  Applied revisions from 2024-11-04 and 2024-11-20
src/genome_sites.c

2025-03-21 11:37:38 -0700 Checking for middle_trdiagonal < querylength.  Applied revision from 2024-11-20
src/trpath-solve.c

2025-03-21 11:37:16 -0700 Checking for middle_univdiagonal < querylength.  Applied revisions from 2024-11-20
src/path-solve.c
src/path-solve.h

2025-03-21 11:12:47 -0700 In Path_solve_junctions, using Splice_resolve_qstart instead of Splice_nomiddle
src/path-solve.c

2025-03-18 18:50:52 -0700 Using Stage1_reset.  Using Stage1_free_computation and Stage1_set_sequence.  Allocating streamspace_alloc once per worker thread.  Calling Stage1_free_sequence.  Applied revisions from 2024-10-02, 2024-10-10, 2024-10-12, 2024-10-13. and 2024-10-16
src/gsnap.c

2025-03-18 18:49:41 -0700 Using Splice_qstart_resolve and Splice_qend_resolve instead of Splice_nomiddle for multiple ends.  Added streamspace_max_alloc and streamspace_alloc as parameters.  Applied revision from 2024-10-12
src/path-solve.c
src/path-solve.h

2025-03-18 18:46:57 -0700 Added streamspace_max_alloc and streamspace_alloc as parameters.  Using nmismatches_allowed from Stage1_T object.  Applied revision from 2024-10-12
src/stage1hr-paired.c
src/stage1hr-paired.h

2025-03-18 18:46:02 -0700 Added streamspace_max_alloc and streamspace_alloc as parameters.  Using mismatch_positions_alloc from Stage1_T object.  Applied revision from 2024-10-12
src/stage1hr-single.c
src/stage1hr-single.h

2025-03-18 18:44:15 -0700 Redefined Stage1_reset to be Stage1_set_sequence.  Moved allocation of streamspace_alloc to worker thread.  Implemented Stage1_free_sequence.  Checking for the case where querylength is zero.  Applied revisions from 2024-09-06, 2024-10-02, 2024-10-10, 2024-10-12, 2024-10-13, 2024-10-16, and 2024-11-20
src/stage1hr.c
src/stage1hr.h

2025-03-18 18:41:12 -0700 Added streamspace_max_alloc and streamspace_alloc as parameters.  Using Univdiag_new_array and Univdiag_free_array instead of individual Univdiag_T elements.  Applied revisions from 2024-10-12 and part of 2024-10-13
src/spliceends.c
src/spliceends.h

2025-03-18 18:39:01 -0700 Added streamspace_max_alloc and streamspace_alloc as parameters.  Applied revision from 2024-10-12
src/pathpair-eval.c
src/pathpair-eval.h

2025-03-18 18:38:12 -0700 Added debugging commands for compute_insertlength.  Using new interface to Path_qstart_resolve and Path_qend_resolve.
src/pathpair.c
src/pathpair.h

2025-03-18 18:37:22 -0700 Fixed Path_genomiclow and Path_genomichigh to ignore altsplice distances
src/path.c

2025-03-18 18:33:22 -0700 Made behavior of Splice_resolve_qstart and Splice_resolve_qend match that of Splice_nomiddle when find_middle_p is false.  Checking for nmismatches and nmatches in the trim region
src/splice.c
src/splice.h

2025-03-18 18:29:56 -0700 Using std memorypool for Indelinfo_T.  Applied revision from 2024-10-12
src/indel.c

2025-03-18 18:28:50 -0700 Added streamspace_max_alloc and streamspace_alloc as parameters
src/concordance.c
src/concordance.h

2025-03-18 18:28:29 -0700 Added streamspace_max_alloc and streamspace_alloc as parameters
src/trpath-convert.c
src/trpath-convert.h

2025-03-18 18:27:17 -0700 Reverted changes that required alignment to within END_SUPPORT of the read ends
src/trpath-solve.c

2025-03-18 18:26:47 -0700 Clarified parameter to be read_nmismatches_allowed
src/tr-extension-search.c
src/tr-extension-search.h

2025-03-18 18:21:50 -0700 Formatting change.  Applied revision from 2024-10-20
src/merge-diagonals-simd-uint4.c

2025-03-18 18:19:45 -0700 Checking for a single stream having no elements, or a multiple streams having a total of zero elements
src/merge-diagonals-heap-uint4.c
src/merge-diagonals-heap-uint8.c
src/merge-diagonals-simd-uint4.c
src/merge-diagonals-simd-uint8.c

2025-03-18 18:17:53 -0700 Using macros from merge-method.h.  Applied revision from 2024-10-12
src/segment-search.c

2025-03-18 18:15:46 -0700 Added streamspace_max_alloc and streamspace_alloc as parameters.  Applied revision from 2025-03-18
src/path-fusion.h

2025-03-18 18:14:46 -0700 Added streamspace_max_alloc and streamspace_alloc as parameters.  Applied revision from 2024-10-12
src/localdb-read.c
src/localdb-read.h

2025-03-18 18:13:38 -0700 Using macros from merge-method.h.  Applied revision from 2024-10-12
src/kmer-search.c

2025-03-18 18:10:45 -0700 Defined Reader_new to set only oligosize, so it can be reused.  Implemented Reader_set_sequence.  Applied revisions from 2024-10-10 and 2024-10-13
src/reader.c
src/reader.h

2025-03-18 18:08:46 -0700 Using Univdiag_new_array and Univdiag_free_array, instead of individual Univdiag_T elements.  Applied revision from 2024-10-13
src/extension-search.c
src/extension-search.h

2025-03-18 18:07:57 -0700 Using Univdiag_new_array and Univdiag_free_array instead of List_to_array.  Applied revision from 2024-10-13
src/path-fusion.c

2025-03-18 11:34:37 -0700 Commented out Univdiagpool_push_univdiag and Univdiagpool_free_univdiag, since we are using Univdiag_new_array and Univdiag_free_array instead.  Applied revision from 2024-10-13
src/univdiagpool.c
src/univdiagpool.h

2025-03-18 11:31:43 -0700 Implemented Univdiag_new_array and Univdiag_free_array.  Applied revision from 2024-10-13
src/univdiag.c
src/univdiag.h

2025-03-18 11:29:09 -0700 Implemented Univdiag_new_array_keep.  Applied revision from 2024-10-10
src/univdiag.c
src/univdiag.h

2025-03-14 16:22:44 -0700 Moved allocation of novel_univdiags_alloc, novel_diagonals_alloc, and localdb_alloc from Stage1 read procedures to worker threads.  Applied revision from 2024-10-08
src/gsnap.c

2025-03-14 16:10:48 -0700 Moved allocation of novel_univdiags_alloc, novel_diagonals_alloc, and localdb_alloc from Stage1_read procedures to worker threads.  Applied revision frmo 2024-10-08
src/stage1hr-paired.c
src/stage1hr-paired.h
src/stage1hr-single.c
src/stage1hr-single.h

2025-03-14 15:37:49 -0700 Using new interface to MALLOC_ALIGN.  Applying revision from 2024-10-12
src/intersect-small.c
src/merge-uint4.c
src/merge-uint8.c
src/path.c
src/transcriptome-search.c

2025-03-14 15:30:42 -0700 Changed macros to use new procedures for allocating and freeing aligned space.  Applied revisions from 2024-10-12
src/mem.h

2025-03-14 15:28:14 -0700 Added new procedures for allocating and freeing aligned space.  Applied revision from 2024-10-12
src/mem.c

2025-03-14 15:25:31 -0700 Made procedures depend upon macros in merge-method.h.  Applied revision from 2024-10-12
src/merge-diagonals-heap-uint4.c
src/merge-diagonals-heap-uint4.h
src/merge-diagonals-heap-uint8.c
src/merge-diagonals-heap-uint8.h
src/merge-diagonals-simd-uint4.c
src/merge-diagonals-simd-uint4.h
src/merge-diagonals-simd-uint8.c
src/merge-diagonals-simd-uint8.h

2025-03-14 14:51:14 -0700 Added code for branchless serial merge, but not using it.  Applied revision from 2024-10-10
src/merge-uint4.c
src/merge-uint8.c

2025-03-14 14:48:42 -0700 Avoiding zero value for max_nstreams.  Applying revision from 2024-11-20
src/mergeinfo.c

2025-03-14 14:47:09 -0700 For Mergeinfo_uint4_T and Mergeinfo_uint8_T, using keep memory pool.  Applied revision from 2024-10-10
src/mergeinfo.c

2025-03-14 14:44:49 -0700 Added new files for merging by heap, and merge-method.h.  Applied revision from 2024-10-12
src/Makefile.dna.am
src/Makefile.gsnaptoo.am

2025-03-14 14:44:22 -0700 Changed filename to merge-diagonals-heap-uint8.  Applied revision from 2024-10-11
src/merge-diagonals-heap-uint8.c
src/merge-diagonals-heap-uint8.h
src/merge-diagonals-heap.c
src/merge-diagonals-heap.h

2025-03-14 14:39:47 -0700 Initial import
src/merge-method.h

2025-03-14 14:35:29 -0700 Implemented Pathpair_uniq.  Applied revision from 2024-09-03
src/pathpair-eval.c
src/pathpair-eval.h

2025-03-11 11:48:45 -0700 Providing a full declaration for a function, needed for compiling on Debian
src/iit-write.c

2025-03-11 11:48:23 -0700 Added a compiler check which requires bool to be an unsigned char
src/bool.h

2025-03-11 11:46:11 -0700 Providing full declaration for a function.  Needed for compiling on Debian
src/iit-write-univ.c

2025-03-11 11:45:16 -0700 Checking whether exon boundaries exceed chrlength
src/get-genome.c

2025-03-11 11:43:42 -0700 Looking for transcriptome files under either transcriptome or genome directories.  Applied part of revision 2024-10-08
src/gsnap.c

2025-03-11 11:11:43 -0700 Transcriptome_trnum returning 0 instead of -1 for a miss.  Applied revision from 2024-10-08
src/transcriptome.c

2025-03-11 11:09:51 -0700 Using 0 instead of -1 for a miss.  Applied revision from 2024-10-08
src/trindex.c

2025-02-28 14:27:21 -0800 Splice_resolve_qstart and Splice_resolve_qend now taking cont_trimpos and cont_nmismatches and comparing solutions against a continuation
src/splice.c
src/splice.h

2025-02-28 14:26:03 -0800 Path_qstart_resolve and Path_qend_resolve using Splice_resolve_qstart and Splice_resolve_qend instead of Splice_nomiddle.  Applied revision from 2024-09-13, but fixed a bug where new_univdiagonal was not being set
src/path-solve.c

2025-02-28 07:04:01 -0800 Using Splice_resolve_qstart and Splice_resolve_qend instead of Splice_resolve.  Redid revision from 2024-08-29
src/path-solve.c

2025-02-28 07:03:26 -0800 Implemented Splice_resolve_qstart and Splice_resolve_qend, which implement lists.  Redid revision from 2024-08-29
src/splice.c
src/splice.h

2025-02-26 21:52:35 -0800 Fixed types for qstart_alts and qend_alts
src/path-solve.c

2025-02-26 21:43:20 -0800 Turned on macro for Path_print
src/path.c

2025-02-26 21:13:48 -0800 Using new interface to Transcriptome_new
src/gsnap.c

2025-02-26 21:13:30 -0800 Turning off a debugging macro
src/path.c
src/trpath-convert.c

2025-02-26 21:13:14 -0800 Handling the possibility that Altsplice_qstart_new or Altsplice_qend_new returns NULL
src/path-solve.c

2025-02-26 21:12:37 -0800 Altsplice_qstart_new and Altsplice_qend_new returning NULL if none of the alternatives passes Splice_accept_p
src/altsplice.c

2025-02-26 21:10:48 -0800 In Splice_accept_p, rejecting if either prob < 0.2
src/splice.c

2025-02-26 21:10:16 -0800 Using new interfaces to Localdb_get procedures
src/spliceends.c

2025-02-26 21:09:52 -0800 In get_exhaustive, accounting for ninserts.  Need anchor_univdiagonal to determine if there is an insertion.  Allowing more solutions from get_exhaustive.  Adopting a different solution from revision 2024-08-29
src/localdb-read.c
src/localdb-read.h

2025-02-26 11:09:49 -0800 Added code for calling Path_segments_good_p, but not using.  Rejecting part of revision from 2024-08-29
src/trpath-convert.c

2025-02-26 11:08:36 -0800 Implementing Path_segments_good_p, but not using.  Rejecting revision from 2024-08-29
src/path.c
src/path.h

2025-02-26 08:59:30 -0800 In Path_eval_and_sort, checking the result of Path_trim_chrbounds and removing the path if excess trimming has occurred
src/path-eval.c

2025-02-26 08:58:39 -0800 In Pathpair_eval_and_sort, checking the result of Path_trim_chrbounds and removing the pathpair if excess trimming has occurred.  Applied revision from 2024-09-09
src/pathpair-eval.c

2025-02-26 08:52:43 -0800 Path_trim_chrbounds checking if endpoints are acceptable and returning a bool.  Applied part of revision 2024-09-09
src/path-trim.c
src/path-trim.h

2025-02-26 08:50:38 -0800 Implemented Path_reverse_nocheck.  Applied part of revision 2024-09-09
src/path.c
src/path.h

2025-02-26 08:41:14 -0800 Implemented List_second_value
src/list.c
src/list.h

2025-02-26 08:40:56 -0800 Defined Univcoordlist_second_value and Univcoordlist_last_elt
src/univcoord.h

2025-02-26 08:40:29 -0800 Implemented Uint8list_second_value
src/uint8list.c
src/uint8list.h

2025-02-26 08:40:12 -0800 Implemented Uintlist_second_value
src/uintlist.c
src/uintlist.h

2025-02-26 08:39:54 -0800 Implemented Intlist_last_elt and Intlist_penultimate_elt
src/intlist.c
src/intlist.h

2025-02-26 08:39:21 -0800 Removed Id keyword
src/genomebits_count.c

2025-02-25 07:20:28 -0800 Making sure that localdb is not used for DNA-seq.  Applied revision from 2024-08-23
src/gsnap.c

2025-02-25 07:15:43 -0800 Moved link files for transcriptome to be under transcriptomedb instead of genomedb.  Changed -C flag to mean transcriptomedb.  Applied revision from 2024-08-20
util/gmap_build.pl.in

2025-02-25 07:12:22 -0800 Using new interface to Transcriptome_new.  Applied revision from 2024-08-20
src/gcount.c

2025-02-25 07:10:51 -0800 Looking for transcriptome in both new location, under transcriptome, and old one, under genome.  Applied revision from 2024-08-20
src/transcriptome.c
src/transcriptome.h

2025-02-25 07:08:42 -0800 Moved info_root under transcriptomedb instead of genomedb.  Applied revision from 2024-08-20
src/trindex.c

2025-02-25 07:05:08 -0800 Added a debugging statement.  Applied revision from 2024-08-20
src/splice.c

2025-02-25 06:57:05 -0800 Checking for 0 value from Transcriptome_trnum.  Applied revision from 2024-10-08
src/knownsplicing.c

2025-02-25 06:54:59 -0800 Fixed calls to EF64_two_ranks in Knownsplicing_intron_p and Knownsplicing_antiintron_p.  Also modified calls in other Knownsplicing procedures.  Applied revision from 2024-08-20
src/knownsplicing.c

2025-02-25 06:51:24 -0800 Added option --splices-noeval.  Applied part of revision 2024-08-15
src/gsnap.c

2025-02-25 06:50:57 -0800 Added splice_evalp to avoid evaluating splices with --splices-noeval is given.  Applied revision from 2024-08-15
src/splice.c
src/splice.h

2025-02-25 06:39:01 -0800 Removed Id strings
src/access.h
src/assert.c
src/assert.h
src/atoi.c
src/atoi.h
src/atoiindex.c
src/bigendian.c
src/bigendian.h
src/bitpack64-access.c
src/bitpack64-access.h
src/bitpack64-incr.c
src/bitpack64-incr.h
src/bitpack64-read.c
src/bitpack64-read.h
src/bitpack64-write.c
src/bitpack64-write.h
src/block.c
src/block.h
src/bool.h
src/boyer-moore.c
src/boyer-moore.h
src/bytecoding.c
src/bytecoding.h
src/bzip2.c
src/bzip2.h
src/cellpool.c
src/cellpool.h
src/changepoint.c
src/changepoint.h
src/chimera.c
src/chimera.h
src/chrnum.c
src/chrom.c
src/chrom.h
src/cmet.c
src/cmet.h
src/cmetindex.c
src/comp.h
src/complement.h
src/compress-write.c
src/compress-write.h
src/cpuid.c
src/cpuid.h
src/datadir.c
src/datadir.h
src/diag.c
src/diag.h
src/diagdef.h
src/diagnostic.c
src/diagnostic.h
src/diagpool.c
src/diagpool.h
src/doublelist.c
src/doublelist.h
src/dynprog.c
src/dynprog.h
src/dynprog_cdna.c
src/dynprog_cdna.h
src/dynprog_end.c
src/dynprog_end.h
src/dynprog_genome.c
src/dynprog_genome.h
src/dynprog_simd.c
src/dynprog_single.c
src/dynprog_single.h
src/except.c
src/except.h
src/filestring.c
src/filestring.h
src/filesuffix.h
src/fopen.c
src/gbuffer.c
src/gbuffer.h
src/genome-write.c
src/genome-write.h
src/genome.h
src/genomicpos.c
src/genomicpos.h
src/get-genome.c
src/getline.c
src/gmapindex.c
src/gregion.c
src/gregion.h
src/iit-read-univ.h
src/iit-read.c
src/iit-read.h
src/iit-write-univ.c
src/iit-write-univ.h
src/iit-write.c
src/iit-write.h
src/iit_dump.c
src/iit_get.c
src/iit_store.c
src/iitdef.h
src/indexdb-cat.c
src/indexdb-write.c
src/indexdb-write.h
src/indexdb.h
src/indexdbdef.h
src/interval.c
src/interval.h
src/intron.c
src/intron.h
src/knownindels.h
src/littleendian.c
src/littleendian.h
src/mapq.c
src/mapq.h
src/match.c
src/match.h
src/matchdef.h
src/matchpool.c
src/matchpool.h
src/maxent.c
src/maxent_hr.c
src/maxent_hr.h
src/md5.c
src/md5.h
src/merge-diagonals-heap.h
src/merge-diagonals-simd-uint4.h
src/merge-diagonals-simd-uint8.h
src/merge-uint4.h
src/merge-uint8.h
src/mode.h
src/oligoindex_hr.c
src/oligoindex_hr.h
src/orderstat.c
src/orderstat.h
src/pair.c
src/pair.h
src/pairdef.h
src/pairpool.c
src/pairpool.h
src/parserange.c
src/parserange.h
src/path-learn.c
src/path-solve.c
src/pbinom.c
src/pbinom.h
src/popcount.c
src/popcount.h
src/request.c
src/request.h
src/result.c
src/result.h
src/sam_sort.c
src/samflags.h
src/samheader.c
src/samheader.h
src/sarray-write.c
src/sarray-write.h
src/scores.h
src/segmentpos.c
src/segmentpos.h
src/semaphore.c
src/semaphore.h
src/separator.h
src/sequence.c
src/sequence.h
src/simplepair.c
src/simplepair.h
src/smooth.c
src/smooth.h
src/snpindex.c
src/splicestringpool.c
src/splicestringpool.h
src/splicetrie.c
src/splicetrie.h
src/splicetrie_build.c
src/stage1.h
src/stage2.c
src/stage2.h
src/stage3.h
src/stopwatch.h
src/table.c
src/table.h
src/tableint.c
src/tableint.h
src/tableuint.h
src/tableuint8.c
src/tableuint8.h

2025-02-25 06:16:48 -0800 Using old interface to Knownsplicing_new
src/support.c

2025-02-25 06:16:04 -0800 Created special setup procedures for localdb.  Applied revision from 2024-08-14
src/path-solve.h
src/spliceends.c
src/spliceends.h
src/stage1hr-paired.c
src/stage1hr-paired.h

2025-02-25 06:15:16 -0800 In calls to Splice_accept_p, values to supporti and supportj are now consistent with splice probs
src/path-solve.c

2025-02-25 06:14:10 -0800 Not using localdb in pass 1.  Applied revision from 2024-08-14
src/gsnap.c

2025-02-25 06:13:12 -0800 Not allowing final mismatch if there are no matches.  Applied revision from 2024-08-13
src/genomebits_trim.c

2025-02-24 18:05:29 -0800 Computing exons after all trimming, instead of incrementally
src/trpath-convert.c

2025-02-24 17:50:54 -0800 Changed assertion.  Applied revision from 2024-08-14
src/transcript.c

2025-02-24 17:19:26 -0800 Added definitions for Univcoordpairtable_T.  Applied revision from 2024-08-12
src/univcoord.h

2025-02-24 17:18:29 -0800 Added comment.  Applied revision from 2024-08-13
src/transcript.c

2025-02-24 17:14:50 -0800 Added better instructions for setting up TGGA.  Applied revision from 2024-08-12
README

2025-02-24 17:13:35 -0800 Fixed to work on NCBI transcriptomes as well as Ensembl.  Applied revision from 2024-08-12
util/gff3_genes.pl.in

2025-02-24 17:08:38 -0800 Reverting to old interface to Knownsplicing_new
src/gsnap.c

2025-02-24 17:08:00 -0800 Implemented Path_qstart and Path_qend.  Applied revision from 2024-08-12
src/path.c
src/path.h

2025-02-24 17:07:09 -0800 Using new interfaces to Altsplice_resolve procedures.  Applied revision from 2024-08-10
src/pathpair.c

2025-02-24 17:06:15 -0800 Using new interface to Splice_accept_p.  Using new interface to Altsplice procedures.  Applying revision from 2024-08-05
src/path-solve.c

2025-02-24 17:04:44 -0800 Using new interface to Splice_accept_p.  Applying revision from 2024-08-05
src/altsplice.c
src/altsplice.h

2025-02-24 17:04:01 -0800 Splice_accept_p using support_tables.  Applying revision from 2024-08-10
src/splice.c
src/splice.h

2025-02-24 17:02:24 -0800 Reverting to old algorithm for compiling known splices.  Revision 2024-08-13 is probably incorrect, as it prevent transcriptome alignments from working
src/knownsplicing.c
src/knownsplicing.h

2025-02-24 14:21:29 -0800 Added code for not performing recursion if path did not extend outermost endpoint (revision from 2024-08-12), but commented out
src/path-solve.c

2025-02-24 14:04:51 -0800 Using new interface to Knownsplicing_new
src/gsnap.c

2025-02-24 14:04:24 -0800 Moved definition of Knownsplicing_T to knownsplicing.h.  No longer rejecting known introns based on counts.  Implemented Knownsplicing_intron_p and Knownsplicing_antiintron_p, used for Support_T.  Applied revisions from 2024-08-13, 2024-08-13, and 2024-08-15
src/knownsplicing.c
src/knownsplicing.h

2025-02-24 14:03:01 -0800 Added support, uintpairtable, uint8pairtable, and splice-count
src/Makefile.dna.am
src/Makefile.gsnaptoo.am

2025-02-24 14:02:09 -0800 Initial import
src/splice-count.c
src/splice-count.h
src/support.c
src/support.h
src/uint8pairtable.c
src/uint8pairtable.h
src/uintpairtable.c
src/uintpairtable.h

2025-02-24 12:46:22 -0800 For mate procedures, checking that qstart < qend.  Computing chrnum properly at the beginning of the genome.  Applied revision from 2024-08-10
src/stage1hr-paired.c

2025-02-24 12:35:22 -0800 Path_endpoints_acceptable_p now disallowing repeats of endpoints.  Applied revision from 2024-08-10
src/path.c

2025-02-24 12:24:18 -0800 Resolve procedures checking whether trimming removes an exon.  Applied revision 2024-08-10
src/path-solve.c

2025-02-24 11:53:53 -0800 Changed assertions about univdiagonals into conditions.  Partial application of revision 2024-08-10
src/path-solve.c

2025-02-24 11:32:17 -0800 Path_eval_nmatches adding altsplice only if nmismatches_known_p is true.  Applied revision from 2024-08-10
src/path-eval.c

2025-02-24 11:11:19 -0800 Accounting for ninserts.  Using Path_trim_qstart_n and Path_trim_qend_n again.  Applying revision from 2024-08-10
src/path-trim.c
src/path-trim.h

2025-02-24 11:10:18 -0800 Added field for nmismatches_known_p from revision 2024-08-10, but not using it
src/altsplice.c
src/altsplice.h

2025-02-24 09:51:25 -0800 Modified debugging statements.  Applied revision from 2024-08-05
src/pathpair.c

2025-02-24 09:23:20 -0800 Removed --end-detail option.  Removed -y and -z abbreviations for --max-insertionlen and --max-deletionlen.  Applied part of 2024-08-05 revision, without changing default values for max insertions or max deletions
src/gsnap.c

2025-02-24 09:07:02 -0800 Short splices are reported as deletions, unless they are known introns.  Reapplied from 2024-07-15
src/junction.c

2024-07-15 11:21:28 -0700 Added option -p to add a prefix before each chromosome name
util/vcf_iit.pl.in

2024-06-20 12:19:24 -0700 Using new interfaces to Spliceends_qstart_trim and Spliceends_qend_trim
src/path-solve.c

2024-06-20 12:18:58 -0700 Spliceends_qstart_trim and Spliceends_qend_trim now taking stage1, novel_univdiags_alloc, novel_diagonals_alloc, and localdb_alloc as parameters
src/spliceends.c
src/spliceends.h

2024-06-17 00:02:34 -0700 Removed extra tokens after #ifdef
src/pathpair-eval.c

2024-06-17 00:02:20 -0700 Using Univcoord_T instead of UINT4
src/extension-search.c

2024-06-16 23:41:30 -0700 Removed obsolete procedures
src/genome_sites.c
src/genome_sites.h

2024-06-16 23:39:27 -0700 Genome_sense_canonical and Genome_antisense_canonical now looking for GT/GC-AG and AT-AC introns
src/genome_canonical.c

2024-06-16 22:52:12 -0700 Defining PRINT_SUB based on CHECK_ASSERTIONS
src/path-print-alignment.c

2024-06-16 22:51:52 -0700 Using new Altsplice procedures
src/path.c

2024-06-16 22:51:40 -0700 Added debugging statements
src/stage1hr-paired.c

2024-06-16 22:51:29 -0700 Pathpair_new_concordant no longer returning some pathpairs as unresolved
src/pathpair.c

2024-06-16 22:51:03 -0700 Not using outerlength as a consideration in local_cmp.  Moved transcript concordance and overlapping to the end of local_cmp
src/pathpair-eval.c

2024-06-16 22:49:50 -0700 Using new Altsplice procedures
src/path-eval.c

2024-06-16 22:49:17 -0700 Using new interface to Trpath_solve_setup
src/gsnap.c

2024-06-16 22:48:54 -0700 Added an assertion
src/genomebits_trim.c

2024-06-16 22:48:41 -0700 Using distal_support instead of (qend - qstart) from univdiag.  Adding best_distali as a field.
src/altsplice.c
src/altsplice.h

2024-06-16 22:47:47 -0700 Using new interfaces to Splice_resolve, Splice_nomiddle, and Altsplice procedures.  Using distal_support from Spliceends procedures instead of (qend - qstart) from univdiag
src/path-solve.c

2024-06-16 22:45:25 -0700 Adding chrhigh as a parameter to Spliceends_qstart_trim and Spliceends_qend_trim
src/spliceends.h

2024-06-16 22:44:22 -0700 In cases of non-extension, checking for a distal indel and returning that univdiag instead with distal_support reflecting both the splice and indel univdiags
src/spliceends.c

2024-06-16 22:42:27 -0700 Using new interfaces to Splice_fusion_sense and Splice_fusion_antisense, which return type
src/path-fusion.c

2024-06-16 22:41:22 -0700 No longer allowing atypical splices, but allowing for AT-AC introns.  Rejecting splices where both probs are less than 0.5
src/splice.c
src/splice.h

2024-06-16 22:38:19 -0700 Now including donor AT and acceptor AC sites, and distinguishing them in a types parameter
src/genome_sites.c
src/genome_sites.h

2024-06-16 22:35:55 -0700 Added tables for AT-AC introns
src/dinucl_bits.c
src/dinucl_bits.h

2024-06-16 17:17:52 -0700 Removed obsolete fields
src/univdiagdef.h

2024-06-16 17:17:43 -0700 Removed comment
src/univdiag.c

2024-06-16 17:17:33 -0700 Not discarding results based on sufficient score or on being a partial alignment
src/trpath-solve.c
src/trpath-solve.h

2024-06-13 14:41:56 -0700 Using new interface to Splice_accept_p and Altsplice procedures
src/path-solve.c

2024-06-13 14:41:36 -0700 Computing medial and distal support without mismatches
src/spliceends.c

2024-06-13 14:40:40 -0700 Using new interface to Splice_accept_p
src/altsplice.c
src/altsplice.h

2024-06-13 13:30:58 -0700 Turned off search for atypical splicing.  Changed region for finding splice sites.  Splice_accept_p using support instead of adj_support, but also checking for good supports on each side
src/splice.c
src/splice.h

2024-06-12 11:09:59 -0700 Added macro for printing sub: field
src/path-print-alignment.c

2024-06-12 11:09:09 -0700 Checking that endpoints are acceptable before calling Trpath_eval_score
src/trpath-solve.c

2024-06-12 11:08:13 -0700 Added debugging information
src/indel.c

2024-06-12 11:08:00 -0700 Making sure best_distal_length is set, even if all distal_probs are zero
src/altsplice.c

2024-06-11 18:50:19 -0700 Computing want_lowest_coordinate_tr_p, instead of genomic want_lowest_coordinate_p
src/trpath-solve.c

2024-06-11 18:49:27 -0700 Pathpair_print now printing chopped_nmatches
src/pathpair.c

2024-06-11 18:49:12 -0700 Added NMATCHES_FACTOR and check for fusions.  If pathL and pathH are contradictory for Path_nmatches_cmp, then use total nmatches
src/pathpair-eval.c

2024-06-11 18:48:05 -0700 Added NMATCHES_FACTOR, CHOPPED_SLOP, and check for fusions
src/path-eval.c

2024-06-11 17:54:49 -0700 Using Path_nmatches_cmp
src/pathpair-eval.c

2024-06-11 17:54:26 -0700 Copying query_compress_fwd and query_compress_rev.  Using new interfaces to Path_create procedure
src/path-fusion.c

2024-06-11 17:53:48 -0700 Using new interface to Path_convert_simple
src/trpath-convert.c

2024-06-11 17:53:31 -0700 Using Path_best_pair_cmp instead of Path_cmp
src/stage1hr-paired.c

2024-06-11 17:53:10 -0700 Implemented Path_eval_nmatches_chopped, Path_nmatches_cmp, and Path_best_pair_cmp
src/path-eval.c
src/path-eval.h

2024-06-11 17:52:36 -0700 Setting chop_qstart and chop_qend before calling Path_best_cmp
src/pathstore.c

2024-06-11 17:51:48 -0700 Removed check for spliceends_qstart and spliceends_qend in Path_resolve procedures
src/pathpair.c

2024-06-11 17:51:16 -0700 Added fields query_compress_fwd, query_compress_rev, chop_qstart, and chop_qend.  Removed fields spliceends_qstart and spliceends_qend
src/path.c
src/path.h

2024-06-11 17:50:11 -0700 Using new interface to Splice_accept_p
src/path-solve.c

2024-06-11 17:49:17 -0700 Handling the case where nunivdiagonals is zero
src/extension-search.c

2024-06-11 17:48:59 -0700 Added innerp as a parameter.  Using new interface to Splice_accept_p
src/altsplice.c
src/altsplice.h

2024-06-11 17:48:26 -0700 Renamed procedure to be Splice_accept_p, which now takes innerp as a parameter.  Hard-coded max insertionlen and max deletionlen for spliceindels
src/splice.c
src/splice.h

2024-06-11 10:54:43 -0700 Using a different set of rules for huge splices
src/splice.c
src/splice.h

2024-06-11 10:54:09 -0700 Using new interfaces to Trpath_convert procedures
src/concordance.c

2024-06-11 10:53:48 -0700 Added crossover_sense_p to add paths to the other sense if they lack introns
src/trpath-convert.c
src/trpath-convert.h

2024-06-11 10:53:05 -0700 Not evaluating bad splices
src/path-eval.c

2024-06-11 10:52:55 -0700 Not evaluating bad splices
src/pathpair-eval.c

2024-06-11 10:52:34 -0700 Path_setdiff and Path_merge procedures now handling pathstores
src/path.c
src/path.h

2024-06-11 10:51:40 -0700 Using pathstores.  Removing auxinfo objects as they are processed.  Not eliminating auxinfo or pathstores while looping through paired_search_univdiagonals
src/stage1hr-paired.c
src/stage1hr-paired.h

2024-06-11 10:50:04 -0700 Using new interfaces for pathstores.  Using new interfaces to Trpath_convert procedures
src/stage1hr-single.c
src/stage1hr-single.h

2024-06-11 10:49:18 -0700 Added fields for pathstores
src/stage1hr.c
src/stage1hr.h

2024-06-11 10:48:48 -0700 Added pathstore and pathstorepool
src/Makefile.dna.am
src/Makefile.gsnaptoo.am

2024-06-11 10:48:32 -0700 Added pathstorepool
src/gsnap.c

2024-06-11 10:47:58 -0700 Returning pathstores
src/extension-search.c
src/extension-search.h

2024-06-11 10:40:12 -0700 Returning pathstores
src/kmer-search.c
src/kmer-search.h

2024-06-11 10:38:31 -0700 Moved some fields to Pathstore_T object
src/auxinfo.c
src/auxinfo.h

2024-06-11 10:38:06 -0700 Initial import
src/pathstore.c
src/pathstore.h
src/pathstorepool.c
src/pathstorepool.h

2024-06-10 11:20:48 -0700 Spliceindel_resolve now allowing spliceindels at optimal splice probs.  Extending trimpos if remaining distance is less than 8 bp.  Revised Splice_sufficient_probs_p
src/splice.c
src/splice.h

2024-06-10 11:19:15 -0700 Using new interface to Pathpair_eval_and_sort
src/stage1hr-paired.c

2024-06-10 11:18:48 -0700 Allowing for spliceindels in Path_qstart_resolve and Path_qend_resolve
src/path-solve.c

2024-06-10 11:18:13 -0700 Using avg_junction_splice_prob and end_splice_prob
src/path-eval.c

2024-06-10 11:17:57 -0700 Using new interfaces to Path_qstart_resolve and Path_qend_resolve
src/pathpair.c

2024-06-10 11:17:42 -0700 Implemented Pathpair_avg_junction_splice_prob and Pathpair_end_splice_prob
src/pathpair.h

2024-06-10 11:17:15 -0700 Using avg_junction_splice_prob and end_splice_prob
src/pathpair-eval.c
src/pathpair-eval.h

2024-06-10 11:16:41 -0700 Implemented Path_avg_junction_splice_prob and Path_end_splice_prob
src/path.c
src/path.h

2024-06-09 10:57:58 -0700 In Path_qstart_resolve and Path_qend_resolve, looking for a final indel after a splice is added
src/path-solve.c
src/path-solve.h

2024-06-09 07:08:19 -0700 Fixed Spliceends_trim_nosplice procedures to look for local stretches of matches
src/spliceends.c

2024-06-09 06:10:52 -0700 Added fields medial_support and distal_support
src/spliceends.h

2024-06-09 06:10:39 -0700 Computing medial_support and distal_support.  Not allowing spliceends in the case of a non-extension
src/spliceends.c

2024-06-08 18:34:18 -0700 Using Pathpair_overlappingp in Pathpair_local_cmp
src/pathpair-eval.c

2024-06-08 18:34:02 -0700 Implemented Pathpair_overlappingp
src/pathpair.c
src/pathpair.h

2024-06-08 18:33:37 -0700 Using new interface to Splice_resolve and Altsplice_new procedures
src/path-solve.c

2024-06-08 18:24:28 -0700 Storing values for medial support and distal support values
src/altsplice.c
src/altsplice.h

2024-06-08 18:22:53 -0700 Added adj_support parameters to Splice_sufficient_probs_p
src/splice.c
src/splice.h

2024-06-07 16:31:57 -0700 Storing partial trpaths and using them to create univdiagonals.  Requiring that found_score_5 and found_score_3 are better than sufficient scores
src/stage1hr-paired.c

2024-06-07 16:31:04 -0700 Using new interface to Trpath_solve procedures with partialp
src/stage1hr-single.c
src/stage1hr-single.h

2024-06-07 16:30:39 -0700 Added fields partial_sense_trpaths and partial_antisense_trpaths
src/stage1hr.c
src/stage1hr.h

2024-06-07 16:30:21 -0700 Using new interface to Trpath_solve procedures with partialp
src/tr-extension-search.c
src/tr-extension-search.h

2024-06-07 16:30:03 -0700 Returning partialp
src/trpath-solve.c
src/trpath-solve.h

2024-06-07 16:29:40 -0700 Defining Pathpair_junction_splice_prob
src/pathpair.h

2024-06-07 16:29:28 -0700 Checking junction_splice_prob first, and then total_splice_prob
src/path-eval.c
src/pathpair-eval.c

2024-06-07 16:29:04 -0700 Made Splice_sufficient_probs_p an extern function
src/splice.c
src/splice.h

2024-06-07 16:28:43 -0700 Using Splice_sufficient_probs_p
src/path-solve.c

2024-06-07 16:28:28 -0700 Using Splice_sufficient_probs_p
src/altsplice.c
src/altsplice.h

2024-06-07 09:10:07 -0700 Using new interface to Trpath_solve_setup
src/gsnap.c

2024-06-07 09:09:53 -0700 Providing transcript_genestrand information to Trpath_solve procedures, and allowing them to decide on want_lowest_coordinate_p
src/trpath-solve.c
src/trpath-solve.h

2024-06-07 09:09:13 -0700 Added fields for chrnum and transcript_genestrand, and setting them in Trpath_create and Trpath_new procedures
src/trpath.c
src/trpath.h

2024-06-07 09:08:36 -0700 Using chrnum and transcript_genestrand in Trpath_T object
src/trpath-convert.c

2024-06-07 09:06:32 -0700 Using new interfaces to Trpath_solve procedures
src/transcriptome-search.c

2024-06-07 09:06:16 -0700 Using new interfaces to Trpath_solve procedures
src/tr-extension-search.c
src/tr-extension-search.h

2024-06-07 09:06:01 -0700 Using new interfaces to Trpath_solve procedures
src/stage1hr-single.h

2024-06-07 09:05:44 -0700 Turned off TR_ANYPAIR method.  Using new interfaces to Trpath_solve procedures
src/stage1hr-single.c

2024-06-07 09:05:08 -0700 Using new interfaces to Trpath_solve procedures
src/stage1hr-paired.c

2024-06-07 09:04:31 -0700 Added comments
src/spliceends.c

2024-06-07 09:04:17 -0700 Handling multiple medial_qpos in Path_qstart_resolve and Path_qend_resolve
src/path-solve.c
src/path-solve.h

2024-06-07 09:03:27 -0700 Path_structure_cmp now allowing for variations in indel positions
src/path.c

2024-06-07 09:03:03 -0700 Implemented sufficient_probs_p, which allows one bad splice end for short splices
src/splice.c
src/splice.h

2024-06-07 09:02:24 -0700 Pathpair_global_cmp now checking for fusion paths
src/pathpair-eval.c

2024-06-07 09:02:09 -0700 Path_global_cmp now checking for fusion paths
src/path-eval.c

2024-06-07 09:01:26 -0700 Adding debugging statements
src/concordance.c

2024-06-07 09:01:15 -0700 Implemented Altsplice_qstart_best and Altsplice_qend_best.  Adding an optional order_medial_qpos parameter to Altsplice_qstart_new and Altsplice_qend_new
src/altsplice.c
src/altsplice.h

2024-06-06 17:31:30 -0700 Reverting back to resolving over the entire space
src/pathpair.c
src/pathpair.h

2024-06-06 17:26:02 -0700 Allowing poor splice probability to be added to inner side.  For outer altsplices, calling Altsplice_qstart_best and Altsplice_qend_best.  For Path_qstart_resolve and Path_qend_resolve, computing n_good_partners
src/path-solve.c

2024-05-28 17:23:07 -0700 In Path_create, making sure that altsplice splice_qpos is still within the adjacent exon, and not invalidated by trimming
src/path.c

2024-05-20 18:40:25 -0700 Updated for latest version
VERSION
config.site.rosalind.prd

2024-05-20 14:47:04 -0700 On outer altsplices, using Altsplice_select procedures to see if a single best segment can be found and solved
src/path-solve.c

2024-05-20 14:45:50 -0700 Implemented Altsplice_select_qstart and Altsplice_select_qend
src/altsplice.c
src/altsplice.h

2024-05-20 11:35:04 -0700 In Altsplice_resolve procedures, using nmatches instead of nmismatches
src/altsplice.c

2024-05-20 09:52:10 -0700 Made batch level 5 the default
src/gsnap.c

2024-05-20 09:49:40 -0700 Using new interfaces to Splice_resolve and Splice_nomiddle
src/path-solve.c

2024-05-20 09:49:23 -0700 Fixed uninitialized trimpos5 or trimpos3 from spliceindel_resolve.  No longer rejecting splice_qpos from Splice_nomiddle.  Removed parameter check_support_p and added parameter allow_indels_p
src/splice.c
src/splice.h

2024-05-19 19:01:57 -0700 Lowering requirement for outer distal prob from 0.9 to 0.8 (GOOD_DISTAL_PROB)
src/path-solve.c

2024-05-19 19:01:15 -0700 Defining SPLICEINDEL_PROB
src/splice.h

2024-05-19 19:01:03 -0700 For spliceindels, requiring both probs > 0.8 (SPLICEINDEL_PROB), and minimizing number of mismatches.  For splices, requiring either prob >= 0.5
src/splice.c

2024-05-19 14:14:51 -0700 Turned off search for middle exons
src/splice.c

2024-05-19 10:48:09 -0700 Defining GOOD_DISTAL_PROB
src/altsplice.h

2024-05-19 10:47:59 -0700 Filtering for good distal partners in Altsplice_T object
src/altsplice.c

2024-05-19 10:47:33 -0700 Filtering for good distal partners in multiadd procedures
src/path-solve.c

2024-05-19 10:47:10 -0700 Stopped distinction between complete and unextended paths
src/path.c

2024-05-19 10:46:38 -0700 Turned on OMIT_BAD_SPLICES
src/path-eval.c
src/pathpair-eval.c

2024-05-19 07:04:57 -0700 Not adding bad splices on outer side
src/path-solve.c

2024-05-19 07:04:02 -0700 Removed unused variables
src/stage1hr-paired.c

2024-05-19 07:03:19 -0700 If exact splice probs are not the optimal ones, performing spliceindel and comparing the alignments
src/splice.c

2024-05-18 17:39:44 -0700 Computing all splice probs at once in the compute procedures
src/splice.c

2024-05-18 17:38:15 -0700 Computing all splice probs at once in the compute procedures
src/splice.c
src/splice.h

2024-05-18 11:23:40 -0700 Commented out assertions
src/transcriptome-search.c

2024-05-18 11:23:28 -0700 Restored Transcriptome_anypair method
src/stage1hr-single.c

2024-05-18 11:23:13 -0700 Using either mutual concordance or optimal concordance, depending on number of approximate univdiagonal pairs
src/stage1hr-paired.c

2024-05-17 20:59:00 -0700 For unsolved junctions, advancing tr_junctions.  Returning NULL path if trstart or trend are outside of transcript bounds
src/trpath-convert.c

2024-05-17 20:57:42 -0700 In Transcriptome_anypair, performing MALLOC_ALIGN for _sense_trdiagonals and _antisense_trdiagonals
src/transcriptome-search.c
src/transcriptome-search.h

2024-05-17 20:57:03 -0700 Changing field names to _sense_trdiagonals and _antisense_trdiagonals
src/stage1hr.c
src/stage1hr.h

2024-05-17 20:56:27 -0700 Using new field names _sense_trdiagonals and _antisense_trdiagonals
src/stage1hr-single.c

2024-05-17 20:55:40 -0700 When starting genomic search from TGGA, always calling KMER_EXACT1.  Comparing found_score_paired with found_score_5 + found_score_3
src/stage1hr-paired.c

2024-05-17 20:50:44 -0700 Fixed computation of ends of univdiags
src/spliceends.c

2024-05-17 20:49:59 -0700 Assigning nmatches to be -1 before calls to Path_eval_nmatches
src/pathpair.c

2024-05-17 20:49:30 -0700 Implemented Path_completep.  Fixed computation of nmatches in Path_convert_simple
src/path.c
src/path.h

2024-05-17 20:49:01 -0700 Fixed computation of evalp.  Returning nmatches_trimmed, so we can avoid calls to Path_eval_nmatches.  Fixed assignment of values to ends after removing a segment
src/path-trim.c

2024-05-17 20:47:46 -0700 Using Path_completep to assign completep field.  No longer limiting recursive procedure by MAX_DEPTH
src/path-solve.c

2024-05-17 20:46:46 -0700 Checking that nmatches is correct
src/path-eval.c

2024-05-17 20:46:27 -0700 Modified comment
src/localdb-read.c

2024-05-16 17:18:57 -0700 Setting splice_qpos properly for distal segments
src/spliceends.c

2024-05-16 17:05:31 -0700 Putting in temporary code to handle multiple medial splice_qpos
src/path-solve.c

2024-05-16 17:02:12 -0700 Computing pathpairs based on best partners for each side, rather than looking for mutual concordance
src/stage1hr-paired.c

2024-05-16 17:01:29 -0700 Using new interfaces to Altsplice_resolve procedures
src/pathpair.c

2024-05-16 17:01:03 -0700 Prioritizing outerlength before nmatches
src/pathpair-eval.c

2024-05-16 17:00:47 -0700 Using new interface to Altsplice_print
src/path.c

2024-05-16 17:00:35 -0700 Using new interface to Altsplice_qstart_new and Altsplice_qend_new
src/path-solve.c

2024-05-16 17:00:14 -0700 Using new medial_prob field for Altsplice_T
src/path-print-alignment.c

2024-05-16 17:00:02 -0700 Using new medial_prob field for Altsplice_T
src/path-eval.c

2024-05-16 16:59:48 -0700 Using new interface to Altsplice_setup
src/gsnap.c

2024-05-16 16:59:32 -0700 Added debugging statements
src/auxinfo.c

2024-05-16 16:59:21 -0700 Storing only a single value for medial_nmismatches and medial_prob
src/altsplice.c
src/altsplice.h

2024-05-15 15:10:29 -0700 Using Univdiag_new_array to allocate known_univdiags_alloc
src/spliceends.c

2024-05-15 14:16:56 -0700 Using new interfaces to Altsplice_qstart_new and Altsplice_qend_new
src/path-solve.c

2024-05-15 14:16:29 -0700 Using splice_qpos field in Altsplice_T objects
src/path-print-sam.c

2024-05-15 14:16:07 -0700 In Pathpair_resolve, running Path_eval_nmatches if indicated by distal_nmismatches
src/pathpair.c

2024-05-15 14:15:13 -0700 Storing splice_qpos and the distal_qpos values.  In resolve procedures, returning -1 distal nmismatches if they don't match
src/altsplice.c
src/altsplice.h

2024-05-15 12:45:56 -0700 Implemented Univdiag_diagonal_rev_cmp
src/univdiag.c
src/univdiag.h

2024-05-15 12:45:36 -0700 Fixed computation of ninserts, after accounting for flipping of signs in spliceindel_resolve
src/splice.c

2024-05-15 12:45:07 -0700 Merging univdiags in extend procedures
src/spliceends.c

2024-05-15 12:44:43 -0700 Using new interfaces to Altsplice_T procedures
src/path.c

2024-05-15 12:44:32 -0700 Using new interfaces to Altsplice_T procedures
src/path-trim.c

2024-05-15 12:44:15 -0700 Using new interface to Altsplice_T procedures
src/pathpair.c

2024-05-15 12:44:03 -0700 Using new fields in Altsplice_T object
src/path-print-sam.c

2024-05-15 12:43:44 -0700 Storing information as univdiagonals rather than splice positions
src/altsplice.c
src/altsplice.h

2024-05-15 10:24:12 -0700 Reverted last changes using new interfaces to Auxinfo_set_best_paths procedures
src/stage1hr-paired.c

2024-05-15 10:23:46 -0700 Reverted last changes where Auxinfo_set_best_paths procedures freed paths.  Paths are still needed in complete paths lists
src/auxinfo.c
src/auxinfo.h

2024-05-15 09:50:22 -0700 Implemented Univdiag_struct_cmp
src/univdiag.c
src/univdiag.h

2024-05-15 09:50:06 -0700 Added a debugging statement
src/spliceendsgen.c

2024-05-15 09:49:56 -0700 Computing spliceends using univdiags, which improves the endpoints for trimming
src/spliceends.c
src/spliceends.h

2024-05-15 09:48:00 -0700 Removed debugging statement
src/splice.c

2024-05-15 09:47:45 -0700 Handling univdiags from Spliceends procedures
src/path-solve.c

2024-05-15 09:47:04 -0700 Not checking for bad splices
src/pathpair-eval.c

2024-05-15 09:46:51 -0700 Not checking for bad splices
src/path-eval.c

2024-05-15 09:46:23 -0700 Sorting on structs of univdiags rather than pointers
src/localdb-read.c

2024-05-15 09:46:03 -0700 Handling univdiags as input
src/altsplice.c
src/altsplice.h

2024-05-15 09:45:06 -0700 Using new interfaces to Auxinfo_set_best_paths procedures
src/stage1hr-paired.c

2024-05-15 09:44:46 -0700 Auxinfo_set_best_paths procedures now calling Path_free
src/auxinfo.c
src/auxinfo.h

2024-05-14 13:30:29 -0700 Spliceindel_resolve now computing end trims and not re-using nmismatches for Indel_resolve_middle procedures
src/splice.c
src/splice.h

2024-05-14 13:29:14 -0700 Implemented Univdiag_equal and Univdiag_new_array
src/univdiag.c
src/univdiag.h

2024-05-14 13:28:59 -0700 Using new interfaces to Spliceends and Path_solve procedures with univdiags
src/path-eval.c
src/path-fusion.c
src/path-fusion.h
src/path-solve.c
src/path-solve.h
src/pathpair-eval.c
src/pathpair-eval.h
src/pathpair.c
src/pathpair.h
src/stage1hr-paired.c
src/stage1hr-single.c

2024-05-14 13:28:16 -0700 Computing distal segments as univdiags, rather than diagonals
src/spliceends.c
src/spliceends.h

2024-05-14 13:27:46 -0700 Returning univdiags instead of diagonals
src/localdb-read.c
src/localdb-read.h

2024-05-14 13:27:16 -0700 Added comments
src/indel.c

2024-05-14 08:36:21 -0700 Using attach_unknown_qstart and attach_unknown_qend, instead of attach_splice_qstart and attach_splice_qend
src/path-solve.c

2024-05-13 16:51:17 -0700 Calling Trpath_eval_setup
src/gsnap.c

2024-05-13 16:51:04 -0700 Using new interfaces to Trpath_solve procedures
src/stage1hr-paired.c

2024-05-13 16:50:36 -0700 Using new interfaces to Trpath_solve procedures and Tr_extension_search
src/stage1hr-single.c
src/stage1hr-single.h

2024-05-13 16:49:45 -0700 Using new interfaces to Trpath_solve procedures
src/tr-extension-search.c
src/tr-extension-search.h

2024-05-13 16:49:31 -0700 Modified debugging statements
src/trpath.c

2024-05-13 16:49:22 -0700 Requiring a sufficient score on transcriptome-guided alignments
src/trpath-solve.c
src/trpath-solve.h

2024-05-13 16:48:47 -0700 Added trpath-eval.c and trpath-eval.h
src/Makefile.dna.am
src/Makefile.gsnaptoo.am
src/trpath-eval.c
src/trpath-eval.h

2024-05-13 11:13:12 -0700 Fixed bug in calling No alignment instead of Incorrect locus (from 2024-03-07).  Discriminating between inner and outer splices (from 2024-03-11)
src/compare2truth.c

2024-05-13 11:07:05 -0700 Checking for short regions of valid query, where querypos3 < querypos5 (from 2024-05-06)
src/kmer-search.c
src/path-eval.c

2024-05-13 11:03:13 -0700 In combine_leftright_paths, freeing altsplices when trimming (from 2024-03-25)
src/path-solve.c

2024-05-13 10:56:56 -0700 Using new interface to Pathpair_setup
src/gsnap.c

2024-05-13 10:56:42 -0700 In Stage1_init_end_tr, handling the case where the initial state is DONE, from a query sequence with no valid oligos (from 2024-05-03)
src/stage1hr.c

2024-05-13 10:54:33 -0700 Modified debugging statements
src/splice.c

2024-05-13 10:54:07 -0700 Using new interface to Pathpair_resolve
src/pathpair-eval.c

2024-05-13 10:53:49 -0700 Setting values for spliceends_qstart and spliceends_qend
src/path-solve.c

2024-05-13 10:53:18 -0700 Improvements to Pathpair_resolve (from 2024-03-08, 2024-03-11, 2024-03-14, 2024-03-15)
src/pathpair.c
src/pathpair.h

2024-05-13 10:50:42 -0700 Added fields spliceends_qstart and spliceends_qend (from 2024-03-06)
src/path.c
src/path.h

2024-05-13 10:34:55 -0700 In Path_trim_chrbounds, fixed calculation of segments for trimming (from 2024-03-25).  In Path_trim_chrbounds, fixed an issue where remaining univdiagonals is NULL (from 2024-04-23)
src/path-trim.c

2024-05-13 10:18:25 -0700 Considering internal endpoints when comparing alignment structures (from 2024-03-13)
src/path.c
src/path.h

2024-05-13 10:16:50 -0700 Using Path_best_cmp
src/stage1hr-paired.c

2024-05-13 10:16:37 -0700 Implemented Path_best_cmp
src/path-eval.c
src/path-eval.h

2024-05-13 10:15:42 -0700 Using Path_structure_ignore_sense_cmp
src/auxinfo.c

2024-05-13 09:57:26 -0700 Using new interface to Path_print_alignment_setup (from 2024-03-15)
src/gsnap.c

2024-05-13 09:56:41 -0700 Computing deletionpos at print time (from 2024-03-11).  Printing splicesites correctly at the ends of alignment, and reporting medial prob of an altsplice (from 2024-03-13).  Added sub: field in output (from 2024-03-15)
src/path-print-alignment.c
src/path-print-alignment.h

2024-05-13 09:54:58 -0700 Computing deletionpos at print time (from 2024-03-11)
src/path-print-sam.c

2024-05-13 09:53:54 -0700 No longer calling Junction_set_deletionpos (from 2024-03-11)
src/path-trim.c

2024-05-13 09:53:10 -0700 Using new interface to Junction_new_deletion  (from 2024-03-11)
src/path-solve.c
src/trpath-solve.c

2024-05-13 09:52:38 -0700 Removed deletionpos as a field.  Returning a deletion junction if splice distance is short (from 2024-03-11)
src/junction.c
src/junction.h

2024-05-13 09:37:52 -0700 Fixed an issue leading to 0M (from 2024-03-06).  Using dinucleotides at medial splice sites, rather than medial probability (from 2024-03-11).  Scanning through all diagonals to find best distal prob (from 2024-03-13).  Fixed initialization of max_medial_setp (from 2024-05-03).
src/spliceends.c
src/spliceends.h

2024-05-13 09:16:17 -0700 Implemented fill_splicesites procedures (from 2024-03-11)
src/genome_sites.c
src/genome_sites.h

2024-05-13 08:41:08 -0700 Added bounding information to Altsplice_print (from 2024-03-13)
src/altsplice.c

2024-05-13 08:38:05 -0700 For insertions in geneminus transcripts, subtracting ninserts from the genomic endpoint (from 2024-04-16)
src/trpath-convert.c

2024-05-13 08:33:46 -0700 Transcript_list_sort now removes duplicate transcripts (from 2024-05-07)
src/path-eval.c
src/transcript-remap.c
src/transcript.c
src/transcript.h

2024-05-13 08:27:29 -0700 For get_by_ends method, allowing no mismatches (from 2024-03-13)
src/localdb-read.c

2024-05-13 08:25:31 -0700 Added a debugging statement (from 2024-05-03)
src/oligo.c

2024-05-13 08:24:12 -0700 Fixed debugging statement (from 2024-03-07)
src/merge-diagonals-simd-uint4.c

2024-05-13 08:22:45 -0700 Implemented Intlist_last_value_set (from 2024-03-13)
src/intlist.c
src/intlist.h

2024-05-13 08:21:15 -0700 Modified debugging statement (from 2024-03-07)
src/intersect-lower-large.c

2024-05-13 08:21:05 -0700 Removed faulty assertions (from 2024-03-07)
src/intersect-lower-small.c

2024-05-13 08:18:05 -0700 Added debugging statements (from 2024-03-13)
src/hitlistpool.c

2024-05-13 08:15:57 -0700 On a failed mmap, printing the strerror message (from 2024-03-06)
src/access.c

2024-02-25 16:33:37 -0800 Commented out Transcript_list_trim, used previously when Path_consolidate used Path_common_structure_p
src/transcript.c
src/transcript.h

2024-02-25 16:32:49 -0800 In finding knownsplicing, checking for pos5 equaling pos3, which can happen with spliceends starting at middle_genomicpos and alternating sides
src/knownsplicing.c

2024-02-25 16:31:29 -0800 Checking for trimpos being equal to splice_qpos, meaning the lack of a partner, and giving rise to 0M before a splice
src/spliceends.c

2024-02-25 16:30:39 -0800 Trimming even if the path came from a transcript.  Using new interfaces to Path_trim procedures
src/pathpair-eval.c

2024-02-25 16:29:51 -0800 No longer using MIN_END.  When trimming a segment, freeing transcripts for that path.  Commented out Path_trim_qstart_n and Path_trim_qend_n, used previously by Path_consolidate with Path_common_structure_p
src/path-trim.c
src/path-trim.h

2024-02-25 16:28:22 -0800 In Path_consolidate, using Path_structure_cmp instead of Path_common_structure_p
src/path-eval.c

2024-02-25 16:27:38 -0800 Moved Path_common_structure_p to path-eval.c
src/path.c
src/path.h

2024-02-22 09:54:51 -0800 Initialized auxinfo_gplus and auxinfo_gminus, which otherwise could lead to an improper free
src/stage1hr-single.c

2024-02-22 09:54:05 -0800 Added salvage for distal and medial splice sites, if nothing else is found
src/spliceends.c

2024-02-22 09:53:25 -0800 Removed support based solely on length.  Checking for two bad splice probs
src/splice.c

2024-02-22 09:52:35 -0800 Added a debugging statement
src/junction.c

2024-02-22 08:12:40 -0800 Added a debugging statement
src/splice.c

2024-02-22 08:12:28 -0800 Assigning donor and acceptor probs correctly by comparing plus and sense_forward_p
src/pathpair.c

2024-02-22 08:12:00 -0800 Assigning donor and acceptor probs correctly by comparing plusp and sense_forward_p
src/path-solve.c

2024-02-22 08:11:33 -0800 Handling cases without partner using max_medial_prob.  Handling outer cases using min_nmismatches and then max_prob
src/spliceends.c

2024-02-21 18:16:02 -0800 Searching on both sides of middle_genomicpos simultaneously
src/spliceends.c

2024-02-20 16:51:04 -0800 Turned off debugging statements
src/altsplice.c

2024-02-20 16:49:52 -0800 Changed debugging statements
src/spliceends.c

2024-02-20 16:49:13 -0800 Fixed trim_qstart and trim_qend, which always trimmed altsplices
src/path-trim.c

2024-02-20 16:48:37 -0800 Fixed type for best_coord field.  Fixed logic for Altsplice_trim procedures
src/altsplice.c
src/altsplice.h

2024-02-20 10:40:56 -0800 Added comment
src/splice.c

2024-02-20 10:40:44 -0800 Compressed code into more general procedures.  Merged known and novel splices into the same procedure
src/spliceends.c

2024-02-16 08:37:05 -0800 Added intersect-indices-small, needed for Transcriptome_anypair
src/Makefile.dna.am
src/Makefile.gsnaptoo.am

2024-02-16 08:36:49 -0800 Adding setup needed fo Transcriptome_anypair
src/gsnap.c

2024-02-16 08:36:34 -0800 Restored try_repairs.  Always checking support for splices
src/path-solve.c

2024-02-16 08:35:54 -0800 Changed adj_support required for splice probs below 0.80
src/splice.c

2024-02-16 08:34:58 -0800 Restored call to Transcriptome_anypair
src/stage1hr-single.c

2024-02-16 08:34:50 -0800 Restored code for Transcriptome_anypair
src/transcriptome-search.c
src/transcriptome-search.h

2024-02-02 08:55:38 -0800 Using the return values of Path_trim_qstart_trimdiag and Path_trim_qend_trimdiag to determine whether to keep a pathpair.  Formatting changes.
src/pathpair-eval.c

2024-02-02 08:54:51 -0800 Path_trim_qstart_trimdiag and Path_trim_qend_trimdiag now returning a boolean whether the trimming was valid
src/path-trim.c
src/path-trim.h

2024-02-01 07:25:00 -0800 Using new interface to Kmer_segment
src/stage1hr-paired.c
src/stage1hr-single.c

2024-02-01 07:24:31 -0800 Before computing exhaustive univdiagonals, clearing npositions for repetitive oligos and those with large numbers of positions
src/kmer-search.c
src/kmer-search.h

2024-02-01 07:23:40 -0800 Removed assertions
src/intersect-approx-indices-uint4.c

2024-01-31 14:52:58 -0800 Added debugging statements
src/stage1hr-paired.c

2024-01-31 14:52:43 -0800 Removed definitions of Univcoordlist_second_value
src/uint8list.c
src/uint8list.h
src/uintlist.c
src/uintlist.h
src/univcoord.h

2024-01-31 14:52:26 -0800 Fixed loop through univdiagonals for Path_trim_chrbounds
src/path-trim.c

2024-01-31 14:52:00 -0800 Added a Method_string for TR_METHOD
src/method.c

2024-01-31 14:51:49 -0800 In computing univdiags, limiting the number generated
src/kmer-search.c

2024-01-31 09:50:18 -0800 For outer fusions, trimming at outer end and seeing whether the alignment is sufficiently long
src/path-fusion.c
src/path-fusion.h

2024-01-31 09:14:52 -0800 Calling Auxinfo_assign_chrinfo instead of making individual calls to get chrinfo.  Using chrinfo in Auxinfo_T objects to bound searches for mates
src/stage1hr-paired.c
src/stage1hr-single.c
src/stage1hr-single.h

2024-01-31 09:13:02 -0800 Added assertions
src/intersect-approx-indices-uint4.c

2024-01-31 09:12:51 -0800 Not trimming poly-A or poly-T regions for DNA-seq reads.  Using new interfaces to setup procedures
src/gsnap.c

2024-01-31 09:02:00 -0800 Added fields for chrnum, chroffset, and chrhigh.  Implemented Auxinfo_assign_chrinfo
src/auxinfo.c
src/auxinfo.h

2024-01-31 09:01:30 -0800 Implemented procedures to trim at chromosome bounds
src/altsplice.c
src/altsplice.h

2024-01-31 09:00:52 -0800 Implemented Univcoordlist_second_value
src/uint8list.c
src/uint8list.h
src/uintlist.c
src/uintlist.h

2024-01-31 09:00:42 -0800 Added macros for Univcoordlist_second_value
src/univcoord.h

2024-01-31 09:00:20 -0800 Path_solve_from_univdiagonal takes chrnum, chroffset, and chrhigh as parameters
src/path-solve.c
src/path-solve.h

2024-01-31 08:59:25 -0800 Filtering alignments with soft clips if --no-soft-clips is given.  Calling Path_trim_chrbounds
src/path-eval.c
src/path-eval.h

2024-01-31 08:58:57 -0800 Filtering alignments with soft clips if --no-soft-clips is given.  Calling Path_trim_chrbounds
src/pathpair-eval.c
src/pathpair-eval.h

2024-01-31 08:57:57 -0800 Not allowing main_univdiagonal to go below 0
src/path.c

2024-01-31 08:57:34 -0800 Implemented Path_trim_chrbounds to replace previous trimbounds procedures.  Using evalp to determine whether Path_eval_nmatches needs to be called
src/path-trim.c
src/path-trim.h

2024-01-29 10:10:03 -0800 Fixed typo
src/stage1hr-paired.c

2024-01-29 09:30:10 -0800 Keeping track of complete5_p and complete3_p, and using them to decide globally for finding pathpairs.  Turned on filterp again for Pathpair_eval_and_sort.  Using paths_mates procedures and not univdiagonals_mates procedures
src/stage1hr-paired.c

2024-01-29 09:21:16 -0800 Added fields complete_sense_p and complete_antisense_p
src/auxinfo.c
src/auxinfo.h

2024-01-29 06:26:31 -0800 After exhaustive method, using unresolved methods from that method if necessary.  Not using unresolved methods, if there more than 100 of them.  Turned off filterp for Pathpair_eval_and_sort
src/stage1hr-paired.c

2024-01-29 06:24:46 -0800 For global_cmp, checking for coverage before nbadsplices
src/pathpair-eval.c

2024-01-29 06:24:25 -0800 For global_cmp, checking for coverage before nbadsplices
src/path-eval.c

2024-01-29 06:22:14 -0800 Checking that large introns are not split on alignments that are already a chimera
src/gmap.c

2024-01-28 15:33:41 -0800 Using new field names in Altsplice_T objects
src/path-eval.c

2024-01-28 15:33:16 -0800 In Pathpair_resolve, using new information provided by Altsplice_resolve procedures
src/pathpair.c

2024-01-28 15:32:33 -0800 Using new field names in Altsplice_T objects
src/path.c

2024-01-28 15:31:59 -0800 Handling multiple different splice_qpos from Spliceends procedures
src/path-solve.c

2024-01-28 15:31:00 -0800 Spliceends_T objects now allowing for different splice_qpos and distal lengths
src/spliceends.c
src/spliceends.h

2024-01-28 15:29:51 -0800 Handling differing splice_qpos and medial_nmismatches.  Recording anchor_qpos.  Sorting distal positions
src/altsplice.c
src/altsplice.h

2024-01-28 15:27:36 -0800 Removed assertion in atypical_splice comparing splice_querypos_low and splice_querypos_high
src/splice.c

2024-01-27 12:50:43 -0800 Using new field names for Auxinfo_T objects
src/stage1hr.c

2024-01-27 12:50:28 -0800 Using new interface to Splice_resolve.  Path_extend calls Path_eval_nmatches.  Removed Path_add_junctions
src/path-solve.c

2024-01-27 12:49:29 -0800 Performing get_by_sarray, then get_by_ends, and then get_exhaustive until we get results
src/localdb-read.c
src/localdb-read.h

2024-01-27 12:48:59 -0800 Changed name of procedure to be Kmer_compute_auxinfo_univdiags
src/kmer-search.c
src/kmer-search.h

2024-01-27 12:48:35 -0800 For univdiagonals, setting best paths only after we check genome-wide for complete paths
src/stage1hr-paired.c

2024-01-27 12:47:38 -0800 Changed names of fields to specify complete paths.  Implemented separate procedures for setting best sense and antisense paths
src/auxinfo.c
src/auxinfo.h

2024-01-27 12:46:28 -0800 Using trimmedp information from Localdb_get.  Ensuring that results of trim_5 and trim_3 are sorted.  Making order of results for Spliceends_qstart_resolve and Spliceends_qend_resolve match those of trim_5 and trim_3
src/spliceends.c
src/spliceends.h

2024-01-27 12:44:45 -0800 Performing final inversion in Splice_resolve, before checking bounds.  Removed salvagep as a parameter
src/splice.c
src/splice.h

2024-01-27 12:43:49 -0800 Using new names for Altsplice_resolve procedures
src/pathpair.c

2024-01-27 12:43:33 -0800 Using new field names for Altsplice_T objects
src/path-print-sam.c
src/path-trim.c

2024-01-27 12:42:47 -0800 Changed names of fields.  Improved Altsplice_resolve procedures to consider distal probs
src/altsplice.c
src/altsplice.h

2024-01-26 16:45:15 -0800 Providing trimmedp as output
src/localdb-read.c
src/localdb-read.h

2024-01-26 10:08:14 -0800 Removed obsolete command-line parameters.  Changed expected_pairlength to be 1000.  Using new interfaces to setup procedures
src/gsnap.c

2024-01-26 10:07:39 -0800 Using new interface to Path_solve_from_diagonals
src/extension-search.c

2024-01-26 10:05:15 -0800 Using new interface to Path_solve_junctions
src/trpath-convert.c
src/trpath-convert.h

2024-01-26 10:05:04 -0800 Providing max_insertionlen and max_deletionlen at setup, rather than as parameters
src/trpath-solve.c
src/trpath-solve.h

2024-01-26 10:03:54 -0800 Using concordance_distance.  Removed anchored procedures.  Removed max_insertionlen, max_deletionlen, and overall_distance as parameters
src/stage1hr-paired.c
src/stage1hr-paired.h

2024-01-26 10:03:11 -0800 Removed max_insertionlen, max_deletionlen, and overall_distance as parameters
src/concordance.c
src/concordance.h
src/path-fusion.c
src/path-fusion.h
src/pathpair-eval.c
src/pathpair-eval.h
src/stage1hr-single.c
src/stage1hr-single.h

2024-01-26 10:02:33 -0800 Using positive_gap_distance to find spliceends
src/spliceends.c
src/spliceends.h

2024-01-26 10:02:17 -0800 Using positive_gap_distance in Pathpair_resolve
src/pathpair.c
src/pathpair.h

2024-01-26 10:02:01 -0800 Providing positive_gap_distance to Mergeinfo_new procedures
src/stage1hr.c
src/stage1hr.h

2024-01-26 10:01:41 -0800 Changed parameters for Indel_setup
src/indel.c
src/indel.h

2024-01-26 10:01:27 -0800 Changed names of variables for allowed indel lengths
src/genomebits_indel.c
src/genomebits_indel.h

2024-01-26 10:01:04 -0800 Providing max_insertlength at setup
src/altsplice.c
src/altsplice.h

2024-01-26 10:00:37 -0800 Providing max_insertionlen and max_deletionlen at setup, instead of in parameters.  Removed Kmer_anchored procedures.  Checking for splicingp before calling Spliceends_trimmed procedures
src/extension-search.c
src/extension-search.h
src/kmer-search.c
src/kmer-search.h
src/path-solve.c
src/path-solve.h
src/splice.c
src/splice.h
src/tr-extension-search.c
src/tr-extension-search.h

2024-01-26 09:59:10 -0800 Using new interface to Trpath_solve_from_diagonals
src/transcriptome-search.c

2024-01-26 09:53:32 -0800 In new procedures, changed parameter name to be max_localdb_distance
src/mergeinfo.c
src/mergeinfo.h

2024-01-26 09:52:52 -0800 Changed assertion
src/localdb-read.c

2024-01-26 09:51:50 -0800 Modified debugging statement
src/intersect-approx-indices-uint4.c

2024-01-25 12:30:32 -0800 For singlepaths, performing solve_all if necessary
src/stage1hr-paired.c

2024-01-25 12:30:08 -0800 Fixed computation of trimpos for known splicesites
src/spliceends.c

2024-01-25 11:10:14 -0800 Removed Splice_resolve_fusion
src/splice.h

2024-01-25 11:10:05 -0800 In Splice_fusion procedures, fixed non-return of a value
src/splice.c

2024-01-25 11:09:42 -0800 Checking for correct sense before calling outer fusion procedures
src/pathpair-eval.c

2024-01-25 11:09:23 -0800 Turned off remapping and repairing of paths in TGGA mode, which seems to slow down program significantly
src/path-solve.c

2024-01-25 11:08:58 -0800 Implemented single-end splicing with Splice_fusion_sense and Splice_fusion_antisense
src/path-fusion.c

2024-01-25 11:08:26 -0800 Fixed bugs with AVX512 code
src/intersect-indices2-small.c

2024-01-24 16:49:58 -0800 Making calls for outer fusions to Splice_fusion_sense and Splice_fusion_antisense
src/path-fusion.c

2024-01-24 16:48:33 -0800 Fixed invert_mismatch_positions and invert_sites.  Implemented Splice_fusion_sense and Splice_fusion_antisense
src/splice.c
src/splice.h

2024-01-24 10:11:33 -0800 Using intersect-indices2 procedures instead of intersect-indices
src/gsnap.c

2024-01-24 10:11:08 -0800 Removed include of path-solve.h
src/path-fusion.c

2024-01-24 10:10:52 -0800 Using new interface to Stage1_fill_all_positions_gen.  Checking that localdb is not NULL before running novel indel procedures
src/spliceends.c

2024-01-24 10:10:16 -0800 Removed obsolete code for genome-based concordance
src/concordance.c

2024-01-24 10:09:37 -0800 Removed include of intersect-indices-small
src/transcriptome-search.c

2024-01-24 10:09:21 -0800 Stage1_fill_all_positions_gen now returning total_npositions instead of max_npositions
src/stage1hr.c
src/stage1hr.h

2024-01-24 10:08:38 -0800 Using new interface to Stage1_fill_all_positions_gen and Kmer_segment
src/stage1hr-single.c

2024-01-24 10:08:15 -0800 For mate procedures, storing count and bestk results in auxinfo.  For single-end results, appending results of Path_extend
src/stage1hr-paired.c

2024-01-24 10:06:59 -0800 Added fields mate_count and mate_bestk
src/auxinfo.h

2024-01-24 10:06:37 -0800 Using intersect-indices2-small and intersect-indices2-large instead of intersect-indices-small and intersect-indices-large
src/Makefile.dna.am
src/Makefile.gsnaptoo.am

2024-01-24 10:05:59 -0800 Making results unique from Kmer_exact1
src/kmer-search.c

2024-01-24 10:05:43 -0800 Initial import
src/intersect-indices2-large.c
src/intersect-indices2-large.h
src/intersect-indices2-small.c
src/intersect-indices2-small.h

2024-01-24 09:30:47 -0800 In get_records_gplus and get_records_gminus, using code without a branch inside the loop
src/kmer-search.c
src/kmer-search.h

2024-01-23 16:11:28 -0800 Fixed call to Merge_diagonals_large
src/kmer-search.c

2024-01-23 16:11:12 -0800 Commented out unused variables
src/intersect-concordance-uint4.c
src/intersect-concordance-uint8.c

2024-01-23 16:10:59 -0800 Edited comment
src/splice.c

2024-01-23 16:10:38 -0800 Cleaned up code
src/merge-diagonals-simd-uint4.c
src/merge-diagonals-simd-uint8.c

2024-01-23 16:10:24 -0800 Fixed a memory leak after calling Merge_diagonals
src/spliceends.c

2024-01-23 16:09:34 -0800 Implemented univdiagonals5_mates and univdiagonals3_mates, and using them instead of paths5_mates and paths3_mates
src/stage1hr-paired.c

2024-01-23 16:08:45 -0800 Using mergeinfo_tr for Merge_diagonals
src/transcriptome-search.c

2024-01-23 14:02:57 -0800 Restored use of Spliceendsgen_T rather than Spliceendspool_T
src/Makefile.gsnaptoo.am
src/gsnap.c
src/path-solve.c
src/path-solve.h
src/spliceends.c
src/spliceends.h
src/stage1hr-paired.c
src/stage1hr-paired.h
src/stage1hr-single.c
src/stage1hr-single.h

2024-01-23 14:01:07 -0800 Added debugging code.  Providing vectorpool to Spliceends_new
src/spliceendsgen.c
src/spliceendsgen.h

2024-01-22 13:01:45 -0800 Using the probabilities obtained when finding a middle exon
src/path-solve.c

2024-01-22 13:01:14 -0800 Rejecting a splice if it has low probabilities and low support
src/splice.c

2024-01-22 12:36:54 -0800 Finding pathpairs from the closest mutually best pairs
src/stage1hr-paired.c

2024-01-22 12:36:01 -0800 Implemented Intlist_first_equals_p
src/intlist.c
src/intlist.h

2024-01-22 12:35:18 -0800 Changed values for gminus given to Maxent_hr procedures.  Putting middle_exon procedure after standard splice.  Checking for exon-intron bounds having sufficient matches
src/splice.c

2024-01-22 12:32:44 -0800 Added debugging statements
src/auxinfo.c

2024-01-22 12:32:18 -0800 Using coverage as the first criterion in Pathpair_local_cmp
src/pathpair-eval.c

2024-01-22 12:31:56 -0800 Using coverage as the first criterion in Path_cmp and Path_local_cmp
src/path-eval.c

2024-01-22 12:31:30 -0800 Fixed bug in Path_resolve procedures of pushing the wrong univdiagonal
src/path-solve.c

2024-01-22 08:15:13 -0800 Implemented Splice_nomiddle
src/splice.c
src/splice.h

2024-01-22 08:14:54 -0800 Using new interface to Trpath_convert procedures
src/concordance.c
src/concordance.h
src/stage1hr-paired.c
src/stage1hr-single.c

2024-01-22 08:14:08 -0800 Using new interface to Path_solve_junctions
src/trpath-convert.c
src/trpath-convert.h

2024-01-22 08:13:30 -0800 Using Splice_nomiddle in Path_solve_junctions
src/path-solve.c
src/path-solve.h

2024-01-22 07:26:49 -0800 Using new interface to Stage1_single_read
src/gsnap.c

2024-01-22 07:26:27 -0800 Added a check for improper bounds in compute sites procedures.  Fixed bounds for sites for middle exon
src/splice.c

2024-01-22 07:17:13 -0800 Added comments
src/path-solve.c

2024-01-22 07:17:00 -0800 Using new interface to Trpath_convert procedures, in response to new interface to Path_solve_junctions
src/concordance.c
src/concordance.h
src/stage1hr-paired.c
src/stage1hr-single.c
src/stage1hr-single.h

2024-01-22 07:16:04 -0800 Using new interface to Path_solve_junctions
src/trpath-convert.c
src/trpath-convert.h

2024-01-22 07:12:07 -0800 Added and using field for copying streamsize array before calling Sedgesort_order
src/merge-diagonals-simd-uint4.c
src/merge-diagonals-simd-uint8.c
src/mergeinfo.c
src/mergeinfo.h

2024-01-22 07:11:13 -0800 Declared variables
src/intersect-higher-large.c
src/intersect-lower-large.c

2024-01-22 07:10:57 -0800 Changed variable names
src/genome_sites.c
src/genome_sites.h

2024-01-22 07:10:29 -0800 In Pathpair_resolve, using trimpos information from Altsplice_resolve procedures
src/pathpair.c

2024-01-22 07:09:50 -0800 Handling trimpos information from spliceends.  In resolve procedures, performing a comparison between continuing the univdiagonal and using a new splice.  Using new interface to Splice_resolve
src/path-solve.c
src/path-solve.h

2024-01-22 07:05:06 -0800 Added TR_METHOD
src/method.h

2024-01-22 07:04:47 -0800 Using TR_METHOD to represent a path solved using the transcriptome
src/auxinfo.c

2024-01-22 07:04:06 -0800 Added field alts_trimpos
src/altsplice.c
src/altsplice.h

2024-01-22 07:03:31 -0800 Added trimpos field and returning those values.  Implemented Spliceends_middle_plus and Spliceends_middle_minus
src/spliceends.c
src/spliceends.h

2024-01-22 07:01:49 -0800 Extensive rewrite of splicing code.  Allowing for trimming at ends.  Implemented middle exon.  Utility procedures are now based on querypos rather than qpos
src/splice.c
src/splice.h

2024-01-18 14:24:11 -0800 Using new interface to Auxinfo_gc
src/stage1hr-single.c

2024-01-18 14:23:53 -0800 Made make_pathpairs work by always calling Auxinfo_set_best_paths.  Handling multiple best partners.  Created a separate procedure solve_all
src/stage1hr-paired.c

2024-01-18 14:20:21 -0800 In Pathpair_resolve, using distal bounds instead of main_univdiagonal for making decisions about altsplice
src/pathpair.c

2024-01-18 14:15:49 -0800 In Pathpair_resolve, trimming only if we go past the distal bounds of mate path
src/pathpair-eval.c

2024-01-18 14:15:06 -0800 Allowing for multiple best partners
src/auxinfo.c
src/auxinfo.h

2024-01-18 09:03:36 -0800 Using multiple best paths in auxinfo
src/stage1hr-paired.c

2024-01-18 09:03:06 -0800 Changed atypical_splice to look primarily at support, and then splice prob
src/splice.c

2024-01-18 09:02:39 -0800 In resolve procedures, not requiring splice probs of 0.9
src/path-solve.c

2024-01-18 09:01:47 -0800 Implemented Path_cmp
src/path-eval.c
src/path-eval.h

2024-01-18 09:01:33 -0800 Fixed bug in Compress_queryseq in handling flags
src/compress.c

2024-01-18 09:01:17 -0800 Storing multiple best paths
src/auxinfo.c
src/auxinfo.h

2024-01-17 18:31:36 -0800 Added method for exhaustive search
src/method.c
src/method.h
src/stage1hr-paired.c

2024-01-17 18:25:30 -0800 Changed make_pathpairs to use the best sense/antisense path from auxinfo
src/stage1hr-paired.c

2024-01-17 18:16:13 -0800 In paired_search5_mates and paired_search3_mates, finding and using a global threshold on counts for the mates
src/stage1hr-paired.c

2024-01-17 17:36:05 -0800 Separated procedures to get paired_search5_mates and paired_search3_mates
src/stage1hr-paired.c

2024-01-17 17:28:17 -0800 Formatting change
src/intersect-indices-uint8.c
src/intersect-large.c
src/intersect-small.c

2024-01-17 17:27:57 -0800 Modified comments
src/intersect-wdups-indices.c

2024-01-17 17:27:36 -0800 Fixed issue with reading uninitialized value past end of rare array
src/intersect-approx-indices-uint4.c
src/intersect-approx-indices-uint8.c
src/intersect-approx-uint4.c
src/intersect-approx-uint8.c
src/intersect-concordance-uint4.c
src/intersect-concordance-uint8.c
src/intersect-higher-large.c
src/intersect-higher-small.c
src/intersect-lower-large.c
src/intersect-lower-small.c

2024-01-17 17:13:21 -0800 Replaced spliceendsgen with spliceendspool
src/Makefile.gsnaptoo.am
src/concordance.h
src/gsnap.c
src/kmer-search.h
src/path-fusion.h
src/path-solve.h
src/spliceends.h
src/stage1hr-single.c
src/stage1hr-single.h

2024-01-17 17:12:37 -0800 Fixed issue with memory leaks in Path_merge procedure.  Implemented Path_nbadsplices
src/path.c
src/path.h

2024-01-17 17:11:59 -0800 No longer pruning paths in combine_leftright_paths.  Using information about spliceends that are bounded.  In Path_solve_from_diagonals, always trying without the given qstart_univdiags and qend_univdiags
src/path-solve.c

2024-01-17 17:09:56 -0800 Having different numbers of partners for inner and outer ends.  Returning information about whether partner search was bounded.  Using spliceendspool instead of spliceendsgen
src/spliceends.c

2024-01-17 17:08:53 -0800 Trimming altsplices if they overextend completely, or if they are bounded and did not extend to the mate.  Commented out Pathpair_filter
src/pathpair.c
src/pathpair.h

2024-01-17 17:07:54 -0800 Added a check for bad splices
src/pathpair-eval.c
src/pathpair-eval.h

2024-01-17 17:07:36 -0800 Added a check for bad splices
src/path-eval.c
src/path-eval.h

2024-01-17 17:06:50 -0800 Removed restriction about extending elts if there was significant overlap
src/extension-search.c

2024-01-17 17:06:06 -0800 Implemented Auxinfo_set_best_paths
src/auxinfo.c

2024-01-17 17:05:48 -0800 Added fields for solvedp, best_sense/antisense_partner, and best_sense/antisense_path
src/auxinfo.h

2024-01-17 17:05:09 -0800 Added a boundedp flag and using it to decide whether an altsplice needs to be trimmed.  Not resolving if best insertlength is greater than 400 bp and there are ties
src/altsplice.c
src/altsplice.h

2024-01-17 17:04:09 -0800 Removed unused procedures
src/stage1hr.h

2024-01-17 17:03:35 -0800 Changed from spliceendsgen to spliceendspool
src/stage1hr-paired.h

2024-01-17 17:03:19 -0800 Added paired_search_exhaustive method.  In concordance_univdiagonals, reducing combinatorics by finding best partners for each univdiagonal.  In solve_univdiagonals_auxinfo, making use of the solvedp flag.  Changing from spliceendsgen to spliceendspool
src/stage1hr-paired.c

2024-01-17 16:56:58 -0800 Initial import.  Replaces spliceendsgen
src/spliceendspool.c
src/spliceendspool.h

2024-01-16 17:59:40 -0800 Modified debugging statements
src/extension-search.c

2024-01-16 17:59:22 -0800 Using new procedure Stage1_init_end_tr
src/stage1hr-single.c

2024-01-16 17:59:08 -0800 Setting diagterms at ends
src/stage1hr.c
src/stage1hr.h

2024-01-16 17:58:30 -0800 Changed criterion for end indels and resolves to penalize mismatches by 3
src/spliceends.c

2024-01-16 17:58:04 -0800 Added debugging statements
src/pathpair.c

2024-01-16 17:57:52 -0800 Modified debugging statement
src/path.c

2024-01-16 17:57:40 -0800 Fixed bug with multiple splices to resolve in calling only the nearest univdiagonal and not the others
src/path-solve.c

2024-01-16 16:22:02 -0800 Fixed printing of mate method
src/method.c

2024-01-16 16:21:50 -0800 Added auxinfopool
src/stage1hr-paired.c
src/stage1hr-paired.h
src/stage1hr-single.c
src/stage1hr-single.h
src/stage1hr.c
src/stage1hr.h

2024-01-16 16:21:19 -0800 Using new interface to Auxinfo_new
src/extension-search.c
src/extension-search.h
src/gsnap.c
src/kmer-search.c
src/kmer-search.h

2024-01-16 16:20:48 -0800 Added auxinfopool
src/Makefile.dna.am
src/Makefile.gsnaptoo.am
src/auxinfo.c
src/auxinfo.h
src/auxinfopool.c
src/auxinfopool.h

2024-01-16 14:22:37 -0800 Formatting change
src/mem.c

2024-01-16 14:21:30 -0800 Added fields for exhaustive_counts
src/stage1hr.c
src/stage1hr.h

2024-01-16 14:21:10 -0800 Clarifying aligned variables
src/transcriptome-search.c
src/transcriptome-search.h

2024-01-16 14:20:50 -0800 Annotating aligned variables, and freeing them accordingly
src/stage1hr-single.c

2024-01-16 14:20:25 -0800 Fixed issues with allocating and freeing univdiagonals as aligned.  For mate alignment, finding univdiags
src/stage1hr-paired.c

2024-01-16 14:19:31 -0800 Modified debugging statements
src/spliceends.c

2024-01-16 14:19:17 -0800 Path_merge procedure now handling inputs and outputs as aligned
src/path.c
src/path.h

2024-01-16 14:18:37 -0800 Removed kmer_size as a parameter from Path_solve_from_univdiagonal
src/path-solve.h

2024-01-16 14:18:20 -0800 Path_qstart_resolve and Path_qend_resolve now trimming ends before adding a deletion.  Path_solve_from_univdiagonal now relying on qstart and qend from auxinfo
src/path-solve.c

2024-01-16 14:16:58 -0800 Always returning aligned memory
src/merge-uint4.c
src/merge-uint8.c

2024-01-16 14:16:38 -0800 Clarifying aligned variables
src/merge-diagonals-simd-uint4.c
src/merge-diagonals-simd-uint8.c

2024-01-16 14:16:29 -0800 Always returning aligned memory
src/merge-diagonals-heap.c

2024-01-16 14:16:15 -0800 Annotating aligned memory
src/localdb-read.c

2024-01-16 14:15:54 -0800 Removed unused code.  Ensuring that new univdiagonals are aligned
src/kmer-search.c
src/kmer-search.h

2024-01-16 14:15:19 -0800 Added a parameter alignp to return aligned results
src/intersect-small.c
src/intersect-small.h

2024-01-16 14:14:58 -0800 Returning new univdiagonals as aligned
src/extension-search.c
src/extension-search.h

2024-01-16 10:14:55 -0800 Moved mate method earlier than anchored and added a search for univdiagonals
src/stage1hr-paired.c

2024-01-16 07:11:28 -0800 Removed field extended_paths for Path_T objects
src/stage1hr.c

2024-01-16 07:11:17 -0800 Removed field extended_paths for Path_T objects
src/stage1hr-single.c

2024-01-16 07:11:06 -0800 Removed field extended_paths for Path_T objects
src/stage1hr-paired.c

2024-01-16 07:10:42 -0800 Removed field extended_paths for Path_T objects
src/path-fusion.c

2024-01-16 07:10:21 -0800 Added code for large genomes
src/kmer-search.c

2024-01-16 07:10:07 -0800 Removed field extended_paths
src/path.c
src/path.h

2024-01-16 06:40:13 -0800 Added allocation to handle several localdb regions
src/stage1hr.c
src/stage1hr.h

2024-01-16 06:39:38 -0800 Added comments
src/stage1hr-single.c

2024-01-16 06:39:02 -0800 Added comments
src/stage1hr-paired.c

2024-01-16 06:35:34 -0800 Using new interface to Localdb_get
src/spliceends.c

2024-01-16 06:35:04 -0800 Pathpair_resolve taking a resolve_distance as a parameter
src/pathpair.c
src/pathpair.h

2024-01-16 06:34:31 -0800 Using new interface to Pathpair_resolve
src/pathpair-eval.c

2024-01-16 06:34:05 -0800 Fixed comparison procedures for trnums to allow for the case where transcripts are all invalid
src/path.c

2024-01-16 06:33:38 -0800 Path_solve_from_univdiagonal now takes kmer_size as a parameter.  In combine_leftright_paths, checking that endpoints are monotonic.  Also handling the case where both ends are trimmed, yielding an unknown number of nmismatches
src/path-solve.c
src/path-solve.h

2024-01-16 06:32:19 -0800 Added method LOCAL_MATE
src/method.c
src/method.h

2024-01-16 06:32:09 -0800 Expanding allocation to allow for multiple localdb regions
src/mergeinfo.c
src/mergeinfo.h

2024-01-16 06:31:26 -0800 Implemented procedures for getting one low or one high univdiagonal.  In get_exhaustive, bounding results by low_univdiagonal and high_univdiagonal
src/localdb-read.c
src/localdb-read.h

2024-01-16 06:30:18 -0800 Commented out Kmer_exact2
src/kmer-search.c

2024-01-16 06:30:06 -0800 Modified debugging statement
src/intersect-small.c

2024-01-16 06:29:49 -0800 Using new interface to Stage1hr_paired_setup
src/gsnap.c

2024-01-16 06:29:36 -0800 Modified debugging statements
src/genomebits_count.c

2024-01-16 06:29:23 -0800 Removed field for unsolved_paths.  Added procedures for a single sense or antisense path
src/auxinfo.c
src/auxinfo.h

2024-01-15 16:49:06 -0800 Added genomebits and localdb to setup
src/stage1hr-paired.h

2024-01-15 16:48:49 -0800 Implemented paired_search_singlepaths and using it
src/stage1hr-paired.c

2024-01-15 16:46:01 -0800 Using new interface to Path_solve_from_univdiagonal
src/stage1hr-single.c

2024-01-13 18:47:16 -0800 No longer having a separate shortsplicedist for the ends of the alignment
src/gsnap.c

2024-01-13 18:46:50 -0800 In Path_common_structure_p, now requiring trims at ends to be equal
src/path.c

2024-01-13 18:45:54 -0800 For Transcriptome_exact2 method, taking the union rather than the intersection of each end
src/transcriptome-search.c
src/transcriptome-search.h

2024-01-13 18:45:08 -0800 No longer having a separate shortsplicedist_novelend.  Allocating stream buffer accordingly
src/stage1hr.c

2024-01-13 18:44:36 -0800 No longer having a separate shortsplicedist_novelend
src/stage1hr-single.c
src/stage1hr-single.h

2024-01-13 18:43:54 -0800 No longer having a separate shortsplicedist_novelend.  Allocating stream buffer accordingly.  Fixed some wrong array indices
src/stage1hr-paired.c
src/stage1hr-paired.h

2024-01-13 18:42:38 -0800 No longer having a special shortsplicedist_localdb
src/spliceends.h

2024-01-13 18:42:24 -0800 No longer having a separate shortsplicedist_localdb.  No longer restricting localdb search to be within a single region
src/spliceends.c

2024-01-13 18:40:48 -0800 Checking a second time whether splice_qpos_low < splice_qpos_high.  Removed the requirement for salvagep before looking for an atypical splice
src/splice.c

2024-01-13 18:40:00 -0800 Defined Pathpair_sensedir and Pathpair_total_splice_prob
src/pathpair.h

2024-01-13 18:39:41 -0800 Modified debugging statement
src/pathpair.c

2024-01-13 18:39:12 -0800 Added a step in Pathpair_eval_and_sort to identify the best sensedir
src/pathpair-eval.c

2024-01-13 18:38:46 -0800 Added a step in Path_eval_and_sort to identify the best sensedir
src/path-eval.c

2024-01-13 18:38:09 -0800 Allowing suffix array searches greater than one region (65536)
src/localdb-read.c

2024-01-12 16:28:59 -0800 Removed fields for unsolved paths
src/stage1hr.c
src/stage1hr.h

2024-01-12 16:28:40 -0800 Handling paths with invalid transcripts, coming from calls to Path_solve_junctions by Trpath convert procedures
src/path-eval.c
src/path.c

2024-01-12 16:27:57 -0800 Trpath convert procedures now calling Path_solve_junctions rather than returning unsolved paths
src/concordance.c
src/concordance.h
src/stage1hr-paired.c
src/stage1hr-single.c
src/transcript-remap.c
src/transcript.c
src/transcript.h
src/trpath-convert.c
src/trpath-convert.h

2024-01-12 14:24:17 -0800 Merging sense and antisense paths before consolidate_results.  Using set difference procedures.  Adding provision for KMER_ANCHORED method
src/stage1hr-paired.c

2024-01-12 14:23:06 -0800 Implemented a set difference procedure
src/path.c
src/path.h

2024-01-12 14:22:41 -0800 Now handling cassette differences
src/path-solve.c

2024-01-12 10:25:34 -0800 Added auxinfo.c and auxinfo.h
src/Makefile.dna.am
src/Makefile.gsnaptoo.am

2024-01-12 10:25:18 -0800 Using shortsplicedist rather than shortsplicedist_localb for overall_end_distance
src/gsnap.c

2024-01-12 10:24:43 -0800 Added fields for exhaustive qstart and qend values.  Stage1_fill_all_gen_positions now returns max_npositions_plus and max_npositions_minus
src/stage1hr.c
src/stage1hr.h

2024-01-12 10:23:53 -0800 Using Kmer_segment instead of Kmer_prevalent
src/stage1hr-single.c

2024-01-12 10:23:31 -0800 Improved process for selecting 5' or 3' end to run
src/stage1hr-paired.c

2024-01-12 10:23:02 -0800 Moved SEGMENT1 method after EXT
src/method.c
src/method.h

2024-01-12 10:22:31 -0800 In Kmer_segment, returning univdiagonals with max width or most prevalence
src/kmer-search.c

2024-01-12 10:21:39 -0800 Commented out debugging statement
src/intersect-approx-indices-uint4.c

2024-01-12 10:21:25 -0800 Using new Auxinfo_new_univdiags procedure
src/extension-search.c

2024-01-12 10:21:08 -0800 Changed Aux_new_extension_search to Aux_new_univdiags
src/auxinfo.c
src/auxinfo.h

2024-01-12 10:20:37 -0800 Fixed new merge procedure
src/path.c

2024-01-12 08:15:03 -0800 Using Kmer_segment instead of Kmer_prevalent
src/stage1hr-paired.c

2024-01-12 07:59:12 -0800 Initial implementation of Kmer_segment.  Modified Kmer_anchored_5 and Kmer_anchored_3 to return auxinfos with univdiags
src/kmer-search.c
src/kmer-search.h

2024-01-12 00:28:48 -0800 Implemented Kmer_segment
src/kmer-search.c

2024-01-11 19:07:20 -0800 Implemented a faster procedure for merging
src/path.c

2024-01-11 19:07:01 -0800 In compute_qend_paths, fixed orientation so that previous fwd output to unextended paths, now sent as rev
src/path-solve.c

2024-01-11 17:58:21 -0800 Added fields for extension, qstart, and qend
src/stage1hr.c
src/stage1hr.h

2024-01-11 17:57:51 -0800 Moved single_read_gen_univdiagonals to stage1hr-paired.c
src/stage1hr-single.h

2024-01-11 17:57:33 -0800 Finding fusions.  Moved single_read_gen_univdiagonals to stage1hr-paired.c
src/stage1hr-single.c

2024-01-11 17:56:58 -0800 Handling singlepaths5 and singlepaths3
src/stage1hr-paired.c

2024-01-11 17:55:59 -0800 Using new interface to Pathpair_new_concordant
src/concordance.c
src/concordance.h

2024-01-11 17:55:44 -0800 Added sufficient_matchlength as a criterion to evaluate indels at the ends
src/spliceends.c

2024-01-11 17:55:17 -0800 Pathpair_new_concordant now returning some pathpairs in unresolved_pathpairs
src/pathpair.c
src/pathpair.h

2024-01-11 17:54:44 -0800 Added filterp and check_inner_p as parameters to Pathpair_eval_and_sort
src/pathpair-eval.c
src/pathpair-eval.h

2024-01-11 17:54:16 -0800 Added debugging statements
src/path.c

2024-01-11 17:54:03 -0800 Made compute_qstart_local and compute_qend_local return all paths, and not returning unextended paths
src/path-solve.c

2024-01-11 17:53:08 -0800 Fixed single-end fusion procedures to use extension, qstart, and qend information.  Not relying upon endtrim_allowed, since qstart and qend are approximate
src/path-fusion.c
src/path-fusion.h

2024-01-11 17:52:12 -0800 Added filterp as a parameter to Path_eval_and_sort
src/path-eval.c
src/path-eval.h

2024-01-11 17:51:25 -0800 Created non-aligned memory for prevalent array
src/kmer-search.c

2024-01-11 17:51:01 -0800 Adding extension, qstart, and qend fields to Stage1_T object
src/extension-search.c

2024-01-11 17:50:11 -0800 Fixed return of variable in a void function
src/auxinfo.c

2024-01-11 12:05:31 -0800 No longer filtering paths based on coverage or found score within trims.  Using new interfaces for fusion outer procedures
src/pathpair-eval.c

2024-01-11 12:04:20 -0800 Modified fusion outer procedures to use extension information from extension search in Stage1_T object
src/path-fusion.c
src/path-fusion.h

2024-01-11 10:39:34 -0800 Changed anchoring procedures to return indices
src/kmer-search.c
src/kmer-search.h

2024-01-11 10:39:12 -0800 Using new interface to Path_eval_setup
src/gsnap.c

2024-01-11 10:38:57 -0800 Changed trim_mismatch_score from -4 to -3
src/genomebits_trim.c

2024-01-11 10:38:36 -0800 Using local variables for unextended_paths, rather than storing in Stage1_T object
src/stage1hr-single.c
src/stage1hr-single.h

2024-01-11 10:37:22 -0800 Added univdiagonals/auxinfo fields
src/stage1hr.c
src/stage1hr.h

2024-01-11 10:36:58 -0800 Trpath_solve_from_trdiagonal now using tstart and tend from caller
src/trpath-solve.c

2024-01-11 10:36:24 -0800 Added Univcoordlist_to_array_n
src/univcoord.h

2024-01-11 10:36:02 -0800 Fixed List_to_array_n to return NULL if n is zero
src/uint8list.c
src/uintlist.c

2024-01-11 10:35:34 -0800 Added comments
src/extension-search.c

2024-01-11 10:35:14 -0800 Commented out obsolete Concordance_gen procedure
src/concordance.c
src/concordance.h

2024-01-11 10:34:53 -0800 Removed inline procedures for adding and appending paths
src/auxinfo.h

2024-01-11 10:34:04 -0800 Implemented free, gc, and collect_paths procedures
src/auxinfo.c
src/auxinfo.h

2024-01-11 10:33:40 -0800 Improved Altsplice_print procedure
src/altsplice.c
src/altsplice.h

2024-01-11 10:33:16 -0800 Added concordance procedures for new univdiagonal/auxinfo data structure.  Handling through anchored methods
src/stage1hr-paired.c

2024-01-11 10:32:00 -0800 Restored sending output to lists.  Revised try_repairs to return paths.  Fixed auxinfo endpoints for calls from KMER_PREVALENT
src/path-solve.c
src/path-solve.h

2024-01-11 10:30:28 -0800 Modified debugging statements
src/spliceends.c

2024-01-11 10:30:06 -0800 Fixed splice_qpos for spliceindel_resolve, and calling it
src/splice.c

2024-01-11 10:29:22 -0800 Modified debugging output
src/pathpair.c

2024-01-11 10:28:58 -0800 Removed unused merge and sensedir procedures
src/path.c
src/path.h

2024-01-10 13:57:24 -0800 Storing paths in auxinfo
src/path-solve.h

2024-01-10 13:57:15 -0800 Storing values into auxinfo
src/path-solve.c

2024-01-10 12:29:39 -0800 Initial implementation using univdiagonals and auxinfo
src/stage1hr-paired.c

2024-01-10 12:28:38 -0800 Returning univdiagonals and auxinfo
src/kmer-search.c
src/kmer-search.h

2024-01-10 12:25:37 -0800 Now returning univdiagonals and auxinfo
src/extension-search.c
src/extension-search.h

2024-01-10 12:25:12 -0800 Initial import
src/auxinfo.c
src/auxinfo.h

2024-01-09 12:32:41 -0800 Implement Transcriptome_prevalent method
src/transcriptome-search.c
src/transcriptome-search.h

2024-01-09 12:32:23 -0800 Added fields for tr_plus_diagterms and tr_minus_diagterms
src/stage1hr.c
src/stage1hr.h

2024-01-09 12:32:05 -0800 Added query_compress_fwd and query_compress_rev to next_trdiagonal method
src/stage1hr-single.h

2024-01-09 12:31:45 -0800 Added TR_PREVALENT method
src/stage1hr-single.c

2024-01-09 12:31:19 -0800 Handling single ends correctly after pathpairs are found but eliminated
src/stage1hr-paired.c

2024-01-09 12:30:28 -0800 For finding indels, using separate tests for deletion and insertion.  When innerp is false, requiring distal length to be 4 or more
src/spliceends.c

2024-01-09 12:29:11 -0800 Handling the case where splice sites are found only on segmenti or segmentj, insteading of returning nothing
src/splice.c

2024-01-09 12:28:36 -0800 In Pathpair_resolve, removing altsplices if necessary
src/pathpair.c
src/pathpair.h

2024-01-09 12:28:06 -0800 Adding transcript velocity info
src/path-eval.c

2024-01-09 12:26:33 -0800 Considering outerlength in global_cmp.  Adding transcript velocity info
src/pathpair-eval.c
src/pathpair-eval.h

2024-01-09 12:25:36 -0800 Checking altsplices in computing genomiclow and genomichigh.  Fixed an uninitialized variable
src/path.c
src/path.h

2024-01-09 12:24:59 -0800 Checking supports before attaching an indel
src/path-solve.c

2024-01-09 12:24:14 -0800 Initializing transcriptome_method_p
src/path-fusion.c

2024-01-09 12:23:57 -0800 Added method TR_PREVALENT
src/method.c
src/method.h

2024-01-09 12:23:42 -0800 In get_exhaustive, measuring matchlength by performing trimming
src/localdb-read.c
src/localdb-read.h

2024-01-09 12:22:48 -0800 Excluding exact matches
src/intersect-higher-large.c
src/intersect-lower-large.c

2024-01-09 12:22:30 -0800 Changed assertions
src/genomebits_trim.c

2024-01-09 10:58:11 -0800 Added copyp parameter to Altsplice_new
src/altsplice.c
src/altsplice.h

2024-01-08 08:52:21 -0800 Adjusting shortsplicedist to make sure we don't go past chromosomal bounds
src/spliceends.c

2024-01-08 08:44:29 -0800 Using new interfaces to Path_fusion procedures
src/stage1hr-paired.c

2024-01-08 08:44:13 -0800 Implemented standard extend_trim5 and extend_trim3 procedures, and performing extension within novel_spliceends procedures
src/spliceends.c
src/spliceends.h

2024-01-08 08:43:04 -0800 Using new interfaces to Spliceends procedures
src/path-solve.c

2024-01-08 08:42:44 -0800 Using new interface to Spliceends resolve procedures
src/path-fusion.c
src/path-fusion.h

2024-01-08 08:42:28 -0800 Excluding exact matches
src/intersect-higher-small.c
src/intersect-lower-small.c

2024-01-08 08:42:03 -0800 Treating all mods as a group by computing mod_npositions
src/extension-search.c

2024-01-06 21:09:10 -0800 Removed merge-search and segment-search
src/Makefile.dna.am
src/Makefile.gsnaptoo.am

2024-01-06 21:08:46 -0800 Removed references to Segment_search
src/gsnap.c

2024-01-06 21:08:27 -0800 Removed references to segment-search
src/stage1hr-paired.c
src/stage1hr-single.c

2024-01-06 21:07:56 -0800 Using Spliceends_indel_qstart and Spliceends_indel_qend
src/path-solve.c

2024-01-06 21:07:30 -0800 Implemented Spliceends_indel_qstart and Spliceends_indel_qend
src/spliceends.c
src/spliceends.h

2024-01-06 21:06:24 -0800 Fixed type cast
src/intersect-approx-uint4.c
src/intersect-approx-uint8.c

2024-01-06 21:06:07 -0800 Fixed type cast
src/intersect-approx-indices-uint4.c
src/intersect-approx-indices-uint8.c

2024-01-06 21:05:47 -0800 Fixed type cast
src/intersect-wdups-indices.c

2024-01-06 21:05:36 -0800 Added parameter insertion_slop
src/intersect-higher-large.c
src/intersect-higher-large.h
src/intersect-higher-small.c
src/intersect-higher-small.h
src/intersect-lower-large.c
src/intersect-lower-large.h
src/intersect-lower-small.c
src/intersect-lower-small.h

2024-01-06 09:52:53 -0800 Added field first_read_p
src/stage1hr.c
src/stage1hr.h

2024-01-06 09:50:15 -0800 Using the furthest ends for main_univdiagonal, to allow for cases where only tails overlap
src/path.c

2024-01-06 09:49:18 -0800 Modified debugging statements
src/path-solve.c

2024-01-06 09:48:58 -0800 Fixed typo in debugging statement
src/path-eval.c

2024-01-06 09:48:34 -0800 Added a debugging macro for Kmer_anchored procedures
src/kmer-search.c

2024-01-06 09:48:00 -0800 Fixed debugging output
src/intersect-approx-uint4.c
src/intersect-approx-uint8.c

2024-01-06 09:47:47 -0800 Added comment
src/concordance.c

2024-01-05 16:53:33 -0800 Added comments
src/transcriptome-search.c

2024-01-05 16:53:23 -0800 Performing aligned free where appropriate
src/stage1hr.c
src/stage1hr.h

2024-01-05 16:52:54 -0800 Enabled transcriptome-only alignment
src/stage1hr-single.c

2024-01-05 16:52:43 -0800 Moved genome search code to a separate subroutine.  Enabled transcriptome-only alignment
src/stage1hr-paired.c

2024-01-05 16:52:16 -0800 Limiting sites and partners per site.  Evaluating ends from medial to distal
src/spliceends.c

2024-01-05 16:51:29 -0800 Added debugging statements
src/pathpair.c

2024-01-05 16:51:16 -0800 Not trimming paths if they have a transcriptome method
src/pathpair-eval.c

2024-01-05 16:50:43 -0800 Performing unalias on all altsplice univdiagonals
src/path-trim.c

2024-01-05 16:50:26 -0800 Modified debugging statement
src/path-solve.c

2024-01-05 16:50:14 -0800 Added assertion
src/path-print-sam.c

2024-01-05 16:50:06 -0800 Added assertion
src/path-print-alignment.c

2024-01-05 16:49:44 -0800 Looping through plus and minus separately
src/extension-search.c

2024-01-04 21:08:23 -0800 Using new interfaces to Path_create, Spliceends_qstart_resolve, and Spliceends_qend_resolve
src/path-fusion.c

2024-01-04 21:07:38 -0800 Localdb_get returning sortedp
src/localdb-read.c
src/localdb-read.h

2024-01-04 21:07:09 -0800 Shifting low univdiagonals down by querylength
src/path-trim.c
src/path-trim.h

2024-01-04 21:05:54 -0800 Adjusting low main_univdiagonal down by querylength
src/path.c
src/path.h

2024-01-04 21:04:45 -0800 In deciding to call Path_trim procedures, shifting univdiagonal by querylength
src/pathpair-eval.c

2024-01-04 21:01:50 -0800 Implemented Pathpair_insertlength.  Returning -1U when insertlength cannot be determined.  Making independent decisions to call Path_qstart_resolve and Path_qend_resolve
src/pathpair.c
src/pathpair.h

2024-01-04 20:57:58 -0800 In Splice_resolve, initializing best_donor_prob and best_acceptor_prob
src/splice.c

2024-01-04 20:34:05 -0800 Spliceends_qstart_resolve and Spliceends_qend_resolve now can return multiple diagonals.  Handling of Localdb_get now liits by MAX_NPARTNERS_PER_SITE
src/spliceends.c
src/spliceends.h

2024-01-04 20:32:24 -0800 Handling multiple diagonals returned by Spliceends_qstart_resolve and Spliceends_qend_resolve
src/path-solve.c
src/path-solve.h

2024-01-04 20:30:11 -0800 Using querystart and queryend for KMER_EXACT1 method.  Using diagterm for intersection of univdiagonals to account for usage of the left coordinate for pathL
src/stage1hr-paired.c

2024-01-04 20:28:33 -0800 Using querystart and queryend for KMER_EXACT1 method
src/stage1hr-single.c

2024-01-04 20:28:06 -0800 Stage1_init_end_gen skipping repetitive oligos at ends
src/stage1hr.c
src/stage1hr.h

2024-01-04 20:27:27 -0800 Path_eval_perfect_ends_p starting at querystart and queryend
src/path-eval.c
src/path-eval.h

2024-01-04 20:27:01 -0800 In Kmer_exact1, starting at querystart and queryend to avoid repetitive oligos
src/kmer-search.c
src/kmer-search.h

2024-01-04 20:25:21 -0800 Fixed initial call to scalar_one_set
src/intersect-concordance-uint4.c
src/intersect-concordance-uint8.c

2024-01-04 20:24:31 -0800 Fixed initial call to scalar_one_set
src/intersect-approx-indices-uint4.c
src/intersect-approx-indices-uint8.c

2024-01-04 20:24:07 -0800 Searching based on npositions < MAX_NPOSITIONS at each querypos.  Keeping track of total_npositions separately for plus and minus
src/extension-search.c

2024-01-04 20:22:29 -0800 Modified debugging statements
src/concordance.c

2024-01-03 05:18:41 -0800 Removed merge-search.h and setup.  Using new interface to Stage1hr_single_setup and Stage1hr_paired_setup
src/gsnap.c

2024-01-03 05:17:27 -0800 Added first_read_p as a parameter for conversion procedures
src/trpath-convert.c
src/trpath-convert.h

2024-01-03 05:17:02 -0800 Calling FREE_ALIGN on coords fields
src/stage1hr.c

2024-01-03 05:16:40 -0800 Performing exact search first.  Handling imperfect ends
src/stage1hr-single.c
src/stage1hr-single.h

2024-01-03 05:16:03 -0800 Performing paired exact search first.  Handling imperfect ends
src/stage1hr-paired.c
src/stage1hr-paired.h

2024-01-03 05:14:16 -0800 In resolve procedures, if there are multiple diagonals, returning the lowest or highest result
src/spliceends.c

2024-01-03 05:13:30 -0800 No longer trying to account for querylength, but using only main_univdiagonal.  Pathpair_filter adds a step for insertlength
src/pathpair.c

2024-01-03 05:11:52 -0800 Trimming inner parts before calling resolve procedures.  Comparing each pathpair against the best for local_cmp and global_cmp
src/pathpair-eval.c

2024-01-03 05:10:39 -0800 Using new interface to Path_create.  Handling main_univdiagonal field in Path_T object
src/path-fusion.c

2024-01-03 05:10:08 -0800 In resolve procedures, trimming inner parts
src/path-solve.c
src/path-solve.h

2024-01-03 05:07:27 -0800 Created separate procedures for trimming by position and by univdiagonal
src/path-trim.c
src/path-trim.h

2024-01-03 05:06:22 -0800 Added procedures for main univdiagonal instead of high/low
src/path.c
src/path.h

2024-01-03 04:59:47 -0800 Comparing each path against best for local_cmp and global_cmp
src/path-eval.c

2024-01-03 04:57:57 -0800 Added comment
src/mem.h

2024-01-03 04:57:48 -0800 Added debugging statements
src/localdb-read.c

2024-01-03 04:57:21 -0800 Using new interface to Path_solve_from_ends
src/kmer-search.c
src/kmer-search.h

2024-01-03 04:56:28 -0800 Picking best distances for each rare
src/intersect-concordance-uint4.c
src/intersect-concordance-uint8.c

2024-01-03 04:55:57 -0800 Trying both plus and minus results
src/extension-search.c

2024-01-03 04:55:31 -0800 Using main univdiagonal instead of high/low.  Calling Intersect_concordance with 0 slop
src/concordance.c

2023-12-22 17:40:17 -0800 Added method KMER_PAIRED
src/method.c
src/method.h

2023-12-22 17:40:06 -0800 Changed results of --time to report in microseconds
src/gsnap.c

2023-12-22 17:39:49 -0800 Using new interface to Path_extend
src/concordance.c

2023-12-22 17:39:29 -0800 Fixed debugging procedures
src/intersect-approx-uint4.c

2023-12-22 17:39:17 -0800 Changed Kmer_anchored procedures to return sorted and unique results
src/kmer-search.c
src/kmer-search.h

2023-12-22 17:38:12 -0800 Changed Path_low_univdiagonals and Path_high_univdiagonals to handle a list of paths
src/path.c
src/path.h

2023-12-22 17:37:24 -0800 Fixed some assignments to sensedir in Path_solve_exact.  Changed Path_extend to return either unextended_paths or complete_paths
src/path-solve.c
src/path-solve.h

2023-12-22 17:36:30 -0800 Changed univdiagonals field to prevalent.  Using new interface to Path_extend.  Implemented debugging procedures
src/stage1hr.c
src/stage1hr.h

2023-12-22 17:35:42 -0800 Using clock_gettime for resolution down to nanoseconds
src/stopwatch.c

2023-12-22 17:35:17 -0800 Implemented paired methods that use coords, prevalent, and all_univdiagonals
src/stage1hr-paired.c

2023-12-22 17:34:51 -0800 Reverted to methods from 2021-12-17
src/stage1hr-single.c
src/stage1hr-single.h

2023-12-20 14:42:13 -0800 Modified debugging statements
src/genomebits_kmer.c

2023-12-20 14:41:39 -0800 Removed a debugging statement
src/stage1hr.c

2023-12-20 14:41:11 -0800 Modified comment
src/stage1hr.h

2023-12-20 14:40:47 -0800 In extension procedures, fixed calls to Indexdb_ptr for minus positions to use revcomp oligos
src/spliceends.c

2023-12-19 15:14:31 -0800 Updated for new version
VERSION
config.site.rosalind.prd
config.site.rosalind.tst
share/index.html

2023-12-19 15:08:30 -0800 Stage1_single_read taking first_read_p as a parameter
src/stage1hr-single.h

2023-12-19 15:08:14 -0800 Stage1_single_read taking first_read_p as a parameter
src/stage1hr-single.c

2023-12-19 15:07:45 -0800 Using new interface to next_trdiagonal procedures
src/stage1hr-paired.c

2023-12-19 15:07:20 -0800 In trim5 and trim3, testing querypos for being between 0 and last_querypos.  Testing diagonal for being in the same chromosome
src/spliceends.c

2023-12-19 15:06:16 -0800 Implemented Sedgesort_order_int2
src/sedgesort.c
src/sedgesort.h

2023-12-19 15:06:03 -0800 In Pathpair_new, not creating a pathpair if the chrnums are different
src/pathpair.c

2023-12-19 15:05:41 -0800 In Path_structure_cmp, using effective sensedir instead of the sensedir field to test for equality
src/path.c

2023-12-19 15:05:00 -0800 In Pathpair_eval_and_sort, keeping local hits that are equally good
src/pathpair-eval.c

2023-12-19 15:04:44 -0800 In Path_eval_and_sort, keeping local hits that are equally good
src/path-eval.c

2023-12-19 15:04:02 -0800 Setting a limit on the number of entries in accumulated diagonals
src/kmer-search.c

2023-12-19 15:03:41 -0800 Using new interface to Stage1_single_read
src/gsnap.c

2023-12-19 15:03:12 -0800 Modified debugging statement
src/extension-search.c

2023-12-19 15:02:58 -0800 Adding output for no alignment and for incorrect locus
src/compare2truth.c

2023-12-19 14:28:29 -0800 In Kmer_anypair, computing separate lists of accumulated diagonals for each mod
src/kmer-search.c

2023-12-19 12:52:07 -0800 Kmer_anypair now searches both gplus and gminus for a given querypos
src/kmer-search.c

2023-12-19 11:21:14 -0800 Searching neighboring positions to help avoid missing multiple loci
src/kmer-search.c

2023-12-01 14:50:38 -0800 Fixed criteria for determining reportable alignments
src/gexact.c

2023-11-27 10:41:43 -0800 Initializing univdiagonals to be NULL
src/stage1hr-single.c

2023-11-27 10:41:23 -0800 Calling FREE_ALIGN on coords
src/stage1hr.c

2023-11-27 10:41:03 -0800 No longer allocating a heap entry when nelts in a stream is zero
src/merge-diagonals-simd-uint4.c

2023-11-27 10:40:30 -0800 Turned AVX512 on
src/merge-uint4.c

2023-11-27 10:39:52 -0800 Initializing allocation appropriately.  Fixed checks on whether allocation is needed
src/intersect-approx-indices-uint4.c
src/intersect-approx-indices-uint8.c
src/intersect-approx-uint4.c
src/intersect-approx-uint8.c
src/intersect-concordance-uint4.c
src/intersect-concordance-uint8.c
src/intersect-wdups-indices.c

2023-11-27 10:32:03 -0800 Handling trdiagonals < querylength properly, without assigning a trdiagonal or trnum
src/transcriptome-search.c

2023-11-27 10:31:17 -0800 Added assertion
src/ef64.c

2023-11-20 11:22:10 -0800 Using mergeinfo for transcriptomes
src/transcriptome-search.c

2023-11-20 11:05:01 -0800 Added code for large genomes.  Setting final univdiagonal method to be KMER_EXACT1 for DNA-seq reads
src/stage1hr-paired.c

2023-11-20 11:04:23 -0800 Added final_univdiagonal_method as a parameter to single_read.  Setting final method to be KMER_EXACT1 for DNA-seq reads
src/stage1hr-single.c
src/stage1hr-single.h

2023-11-20 11:03:20 -0800 Fixed typo
src/stage1hr.c

2023-11-20 11:03:07 -0800 Using transcriptome streams
src/transcriptome-search.c

2023-11-20 11:02:45 -0800 Added parameter needed for attach_indel_qstart
src/path-solve.c

2023-11-20 11:02:26 -0800 Added include statements for large genomes
src/merge-search.c

2023-11-20 11:02:06 -0800 Added code for large genomes
src/kmer-search.c

2023-11-19 07:56:01 -0800 Updated for patched version
share/index.html

2023-11-19 07:55:35 -0800 Added new files
src/Makefile.dna.am
src/Makefile.gsnaptoo.am

2023-11-19 07:42:32 -0800 Revised debugging lines
src/genomebits_count.c

2023-11-19 07:42:02 -0800 Checking for low_univdiagonal <= high_univdiagonal before calling localdb procedures
src/path-fusion.c

2023-11-19 07:41:39 -0800 Checking for low_univdiagonal <= high_univdiagonal before calling localdb procedures
src/spliceends.c

2023-11-19 07:40:59 -0800 In updating current paths and coords, removing the special case for non-spliced alignment
src/stage1hr-paired.c

2023-11-19 07:39:51 -0800 Added first_read_p as a paramter to single_read
src/stage1hr-single.h

2023-11-19 07:39:39 -0800 Using correct values of paired_end_p.  Added first_read_p as a parameter.  Terminating paired-end alignment after univdiagonal methods
src/stage1hr-single.c

2023-11-19 07:38:46 -0800 Initializing current set of paths and coords
src/stage1hr.c

2023-11-19 07:38:23 -0800 In combining paths, accounting for insertions
src/trpath-solve.c

2023-11-19 07:37:59 -0800 In combining paths, accounting for insertions.  Checking for extensions beyond the start or end of a chromosome
src/path-solve.c

2023-11-15 18:41:06 -0800 Performing single-read search separately on each end to obtain sufficient score, then performing paired-read search
src/stage1hr-paired.c

2023-11-15 18:40:07 -0800 Formatting changes
src/method.h

2023-11-15 18:39:54 -0800 Checking for coords being aligned
src/concordance.c

2023-11-15 18:39:27 -0800 Removed fields for extended paths
src/stage1hr.c
src/stage1hr.h

2023-11-15 18:39:12 -0800 Changed single_read to return paths in separate lists
src/stage1hr-single.h

2023-11-15 18:36:02 -0800 Changed single_read to return paths in separate lists
src/stage1hr-single.c

2023-11-15 15:26:36 -0800 Implemented Transcriptome_exact2
src/transcriptome-search.c
src/transcriptome-search.h

2023-11-15 15:26:17 -0800 Using trdiagonal methods for single-end reads
src/stage1hr-single.c

2023-11-15 15:04:38 -0800 Added method TR_EXACT2
src/method.c
src/method.h

2023-11-15 15:04:05 -0800 Using new method TR_EXACT1
src/stage1hr-paired.c

2023-11-15 15:03:40 -0800 Added method TR_EXACT2
src/stage1hr-single.c

2023-11-15 15:03:23 -0800 Implemented Stage1_init_end2_positions_tr
src/stage1hr.c
src/stage1hr.h

2023-11-15 14:25:01 -0800 Stopping at KMER_PREVALENCE
src/stage1hr-paired.c

2023-11-15 13:33:14 -0800 No longer updating methods based on found scores.  Updating univdiagonals after each call to Concordance_gen or Path_merge procedures
src/stage1hr-paired.c

2023-11-15 13:29:58 -0800 Implemented Stage1_list_univdiagonals
src/stage1hr.c
src/stage1hr.h

2023-11-15 13:29:23 -0800 Fixed sign on check for completeness
src/trpath-solve.c

2023-11-15 13:29:00 -0800 Setting completep flag
src/trpath-convert.c

2023-11-15 13:28:43 -0800 Added assertions
src/merge-uint4.c
src/merge-uint8.c

2023-11-15 13:28:32 -0800 Added assertion
src/path-solve.c

2023-11-15 13:28:23 -0800 Added functions for low_univdiagonal and high_univdiagonal
src/path.c
src/path.h

2023-11-15 13:27:47 -0800 Allocating coords as aligned memory.  Using new methods Path_low_univdiagonal and Path_high_univdiagonal instead of Path_genomiclow and Path_genomichigh
src/concordance.c

2023-11-14 16:29:03 -0800 Added calls to setup procedures
src/gsnap.c

2023-11-14 16:28:44 -0800 Computing concordance on univdiagonals, and saving them.  Calling fast univdiagonal methods, and then slow ones
src/stage1hr-paired.c

2023-11-14 16:27:22 -0800 Added calls to Kmer_anchored_5, Kmer_anchored_3, and Kmer_widest
src/stage1hr-single.c
src/stage1hr-single.h

2023-11-14 16:26:55 -0800 Fixed types for indices output
src/intersect-approx-indices-uint4.c

2023-11-14 16:26:26 -0800 Added fields for saving all univdiagonals from Kmer_prevalent
src/stage1hr.c
src/stage1hr.h

2023-11-14 16:25:52 -0800 Implemented Path_add_junctions
src/path-solve.c
src/path-solve.h

2023-11-14 16:25:30 -0800 Added methods KMER_PREVALENT, KMER_ANCHOR, and KMER_WIDEST
src/method.c
src/method.h

2023-11-14 16:25:05 -0800 Added parameters to create paths
src/merge-search.h

2023-11-14 16:24:53 -0800 Creating paths by calling Path_add_junctions
src/merge-search.c

2023-11-14 16:24:27 -0800 Added comment
src/merge-diagonals-simd-uint4.c

2023-11-14 16:24:20 -0800 Added another version of Kmer_exact2, but not using it
src/kmer-search.c

2023-11-14 16:23:57 -0800 Initial import
src/intersect-approx-indices-uint8.c

2023-11-14 16:23:47 -0800 Fixed debugging info
src/intersect-approx-uint4.c

2023-11-14 16:23:38 -0800 Changed debugging macro
src/intersect-indices-small.c

2023-11-14 16:23:22 -0800 Initial import
src/intersect-wdups-indices.c
src/intersect-wdups-indices.h

2023-11-14 11:00:00 -0800 Implemented Kmer_prevalent, Kmer_anchored_5, Kmer_anchored_3, and Kmer_widest
src/kmer-search.c
src/kmer-search.h

2023-11-13 16:31:22 -0800 Removed fields for positions at end5 and end3, which were pointers.  Using repetitive_ef64 as a guide for not filling certain oligos.  Added fields for diagterms
src/stage1hr.c
src/stage1hr.h

2023-11-13 16:29:58 -0800 Calling Kmer_exact1, Kmer_anypair, Kmer_exact2, and Kmer_prevalent
src/stage1hr-single.c
src/stage1hr-single.h

2023-11-13 15:36:13 -0800 Implemented Kmer_exact1, Kmer_exact2, and Kmer_prevalent.  Removed qstart and qend information from Kmer_anypair
src/kmer-search.c
src/kmer-search.h

2023-11-12 17:51:25 -0800 Initial implementation
src/merge-search.c
src/merge-search.h

2023-11-11 10:10:02 -0800 Implemented code for merging paths from univdiagonals
src/stage1hr-paired.c

2023-11-11 10:07:46 -0800 Using new interfaces to Path_extend and Path_solve_from_univdiagonal
src/stage1hr-single.c

2023-11-11 10:07:05 -0800 Using new interface to Path_extend
src/stage1hr.c

2023-11-11 10:06:54 -0800 Casting trdiagonal to Univcoord_T
src/trpath-solve.c

2023-11-11 10:06:33 -0800 Using new interface to Path_extend
src/concordance.c

2023-11-11 10:06:23 -0800 Using new interface to Path_solve_from_diagonals
src/extension-search.c

2023-11-11 10:06:00 -0800 Using new interface to Path_solve_from_diagonals
src/kmer-search.c
src/kmer-search.h

2023-11-11 10:05:24 -0800 Using new interface to Path_solve_from_diagonals
src/segment-search.c

2023-11-11 10:03:49 -0800 Using new interfaces to Path_qstart_resolve and Path_qend_resolve
src/pathpair.c

2023-11-11 10:03:31 -0800 Path_solve_from_univdiagonal now takes qstart and qend as parameters.  Removed parameters related to streams
src/path-solve.c
src/path-solve.h

2023-11-10 16:40:42 -0800 Using new interface to Trpath_solve_from_trdiagonal
src/stage1hr-paired.c

2023-11-10 16:40:27 -0800 In Trpath_solve_from_trdiagonal, calling Trpath_solve_from_diagonals if the alignment does not extend to both ends
src/trpath-solve.c
src/trpath-solve.h

2023-11-10 16:21:01 -0800 Changed Univ_IIT_get_trnum to return a Trnum_T
src/iit-read-univ.c

2023-11-10 16:19:51 -0800 Calling setup for Intersect_approx_indices.  Added --show-univdiagonals option
src/gsnap.c

2023-11-10 16:19:25 -0800 Modified comments
src/concordance.c

2023-11-10 16:19:14 -0800 Changed type of Trnum_T to be an unsigned int
src/chrnum.h

2023-11-10 16:18:31 -0800 Performing intersection of trnums
src/stage1hr-paired.c

2023-11-10 16:18:10 -0800 Implemented call to trdiagonal procedures
src/stage1hr-single.h

2023-11-10 16:17:58 -0800 Implemented call to trdiagonal procedures
src/stage1hr-single.c

2023-11-10 16:17:34 -0800 Added fields for storing trdiagonals
src/stage1hr.c
src/stage1hr.h

2023-11-10 16:17:03 -0800 Implemented Trpath_solve_from_trdiagonal
src/trpath-solve.c
src/trpath-solve.h

2023-11-10 16:16:46 -0800 Moved call of Transcriptome_exons inside of Trpath_convert_to_path procedures
src/trpath-convert.c

2023-11-10 16:15:18 -0800 Implemented Transcriptome_anypair.  Revised Transcriptome_exact to return only univdiagonals
src/transcriptome-search.c
src/transcriptome-search.h

2023-11-10 16:14:27 -0800 Added method TR_ANYPAIR
src/method.c
src/method.h

2023-11-10 16:14:05 -0800 Returning only univdiagonals that have sufficient separation
src/kmer-search.c
src/kmer-search.h

2023-11-10 16:13:26 -0800 Added comments
src/intersect-indices-small.c

2023-11-10 16:12:36 -0800 Initial import
src/intersect-approx-indices-uint4.c
src/intersect-approx-indices-uint4.h

2023-11-10 07:45:34 -0800 Moved univdiagonal methods together.  Added code for large genomes
src/stage1hr-paired.c

2023-11-10 07:45:07 -0800 Added code for large genomes
src/kmer-search.c

2023-11-09 17:03:03 -0800 Added back EXT method
src/stage1hr-single.c

2023-11-09 17:02:18 -0800 Checking for density before performing Intersect_approx.  Added back EXT method
src/stage1hr-paired.c

2023-11-09 14:35:05 -0800 When concordance of univdiagonals fails, merging paths from all univdiagonals
src/stage1hr-paired.c

2023-11-09 14:34:27 -0800 Added comments
src/path.c

2023-11-09 14:34:05 -0800 Added option to print coordinates as univdiagonals, rather than chromosomal coordinates
src/path-print-alignment.c
src/path-print-alignment.h

2023-11-09 12:19:58 -0800 Revised exact_univdiagonals fields to be arrays, rather than lists.  In Stage1_fill_all_positions_gen, computing through query_lastpos
src/stage1hr.c
src/stage1hr.h

2023-11-09 12:18:48 -0800 Implemented single_read_next_method_univdiagonal
src/stage1hr-single.h

2023-11-09 12:18:22 -0800 Implemented Path_solve_from_univdiagonal
src/path-solve.c
src/path-solve.h

2023-11-09 12:17:45 -0800 Using Id tag
src/sedgesort.c
src/sedgesort.h

2023-11-09 12:14:25 -0800 Removed unused code
src/spliceends.c

2023-11-09 12:14:12 -0800 Calling univdiagonal methods
src/stage1hr-paired.c

2023-11-09 12:13:30 -0800 Calling univdiagonal methods
src/stage1hr-single.c

2023-11-09 12:08:45 -0800 Fixed values given to Merge_diagonals for gminus.  Specifying len as query_lastpos + 1
src/kmer-search.c

2023-11-09 12:07:14 -0800 Handling the case where nA or nB is 0
src/merge-uint4.c
src/merge-uint8.c

2023-11-09 12:06:58 -0800 Modified comment
src/merge-diagonals-simd-uint8.c

2023-11-09 12:06:47 -0800 Modified comment
src/merge-diagonals-simd-uint4.c

2023-11-09 12:06:33 -0800 Procedures have parameters for below_slop and above_slop
src/intersect-approx-uint4.c
src/intersect-approx-uint4.h
src/intersect-approx-uint8.c
src/intersect-approx-uint8.h

2023-11-09 10:28:21 -0800 Implemented version of Kmer_anypairs_univdiagonals using iterated intersection on accumulated univdiagonals.  In Kmer_exact_univdiagonals, performing merge to return single arrays of univdiagonals
src/kmer-search.c
src/kmer-search.h

2023-11-09 06:22:00 -0800 Initial implementation of Kmer_anypair_univdiagonals.  Made Kmer_exact_univdiagonals have the same interface
src/kmer-search.c
src/kmer-search.h

2023-11-07 08:17:41 -0800 Fixed typo in comment
src/kmer-search.c

2023-11-05 10:18:04 -0800 Performing search through EXT_NOSPLICE, and then finding concordance of unextended paths.  Using new interface to Concordance_gen
src/stage1hr-paired.c

2023-11-05 10:16:16 -0800 Removed call to Kmer_search_end.  Consolidated KMER_EXACT2 into KMER_EXACT1.  Distinguishing between EXT_NOSPLICE and EXT_SPLICE
src/stage1hr-single.c

2023-11-05 10:15:20 -0800 Added code for extending paths using Indexdb_T, not just Localdb_T
src/spliceends.c
src/spliceends.h

2023-11-05 10:14:38 -0800 Renamed shortsplicedist_novelend to shortsplicedist_localdb
src/gsnap.c

2023-11-05 10:14:05 -0800 Added comment
src/list.c

2023-11-05 10:13:53 -0800 Using new interface to Path_solve_from_diagonals
src/extension-search.c
src/extension-search.h

2023-11-05 10:13:16 -0800 Added EXT_NOSPLICE and EXT_SPLICE methods
src/method.c
src/method.h

2023-11-05 10:12:47 -0800 Commented out unused procedures
src/kmer-search.c

2023-11-05 10:12:28 -0800 Using new interface to Path_solve_from_diagonals
src/segment-search.c
src/segment-search.h

2023-11-05 10:11:49 -0800 Setting completep field before returning lists of paths.  Using trimpos info from Spliceends_T object, and handling multiple partners that do not extend to the ends of the alignment
src/path-solve.c
src/path-solve.h

2023-11-05 10:07:54 -0800 Removed field for carryover_paths
src/stage1hr.c
src/stage1hr.h

2023-11-05 10:07:20 -0800 Added a debugging variable
src/pathpair.c

2023-11-05 10:07:07 -0800 Revised merge procedures to separate incomplete and complete paths.  Assigning completep field
src/path.c

2023-11-05 10:06:43 -0800 Added completep field
src/path.h

2023-11-05 10:05:18 -0800 Always assigning extended paths to extended_paths field in Stage1_T object.  Using new merge procedures that separate complete and incomplete paths
src/concordance.c
src/concordance.h

2023-11-05 10:04:01 -0800 Added an assertion
src/altsplice.c

2023-11-03 09:22:06 -0700 Removed the boolean donep
src/genomebits_trim.c

2023-11-03 09:21:44 -0700 Using conservative mode
src/extension-search.c

2023-11-03 09:20:53 -0700 Removing END method to achieve higher speed
src/stage1hr-single.c

2023-11-02 17:59:17 -0700 Fixed type of positions for large genomes in Kmer_search_end
src/kmer-search.c

2023-11-02 16:22:57 -0700 Added debugging statements
src/concordance.c

2023-11-02 16:02:36 -0700 Using values of found_score_5 and found_score_3 instead of pointers.  Fixed direction of sign when checking for anchored_search_5 vs anchored_search_3
src/stage1hr-paired.c

2023-11-02 14:52:47 -0700 Calling Stage1_allocate_carryover
src/stage1hr-paired.c

2023-11-02 14:52:22 -0700 Calling TR_END, and also END method for DNA-seq reads
src/stage1hr-single.c

2023-11-02 14:51:59 -0700 Formatting change
src/extension-search.c

2023-11-02 14:51:51 -0700 Putting new complete paths into the carryover_paths field of the Stage1_T object, rather than trying to integrate them
src/concordance.c

2023-11-02 14:51:17 -0700 Added carryover_paths field and implemented Stage1_allocate_carryover
src/stage1hr.c
src/stage1hr.h

2023-11-02 14:50:32 -0700 No longer taking max_npositions as a parameter to Kmer_search_end
src/kmer-search.c
src/kmer-search.h

2023-11-02 14:50:14 -0700 Using Genomebits_trim procedures instead of Genomebits_consec
src/tr-extension-search.c

2023-11-02 14:49:52 -0700 In nosplice procedures, aborting scoring if the remaining possibility for positive scores is not sufficient for redemption
src/spliceends.c

2023-11-02 14:49:26 -0700 Aborting scoring process if the remaining possibility for positive score is not sufficient for redemption
src/genomebits_trim.c

2023-11-02 12:00:19 -0700 Fixed hard-coded value of 7 instead of kProbe for freq
src/intersect-approx-uint4.c
src/intersect-approx-uint8.c
src/intersect-higher-large.c
src/intersect-higher-small.c
src/intersect-lower-large.c
src/intersect-lower-small.c

2023-11-02 11:59:57 -0700 Fixed bug where result of scalar_one_set was being returned instead of called iteratively
src/intersect-concordance-uint4.c
src/intersect-concordance-uint8.c

2023-11-02 07:06:58 -0700 Using a more aggressive extension with Genomebits_trim rather than Genomebits_consec procedures
src/extension-search.c

2023-11-02 07:06:10 -0700 Hiding binary search from non-SIMD code
src/intersect-approx-uint4.c

2023-11-02 07:06:01 -0700 Fixed assertion.  Hiding binary search from non-SIMD code
src/intersect-approx-uint8.c

2023-11-02 07:05:34 -0700 Using correct macro GETPOS for large genomes
src/kmer-search.c

2023-11-02 07:05:11 -0700 Using new interfaces to Genomebits_trim proceures
src/trpath-solve.c

2023-11-02 07:04:51 -0700 Using new interfaces to Spliceends_trimmed and Genomebits_trim procedures
src/path-solve.c

2023-11-02 07:04:22 -0700 Spliceends_trimmed procedures no longer returning total_nmismatches.  Using new interface to Genomebits_trim procedures
src/spliceends.c
src/spliceends.h

2023-11-02 07:03:29 -0700 Genomebits_trim procedures no longer returning total_nmismatches
src/genomebits_trim.c
src/genomebits_trim.h

2023-11-02 04:57:58 -0700 Updated version number
VERSION
config.site.rosalind.prd
config.site.rosalind.tst

2023-11-02 04:56:39 -0700 Using new interfaces to Trpath_solve_setup and Path_solve_setup
src/gsnap.c

2023-11-02 04:55:54 -0700 Calling Kmer_search_end
src/stage1hr-single.c

2023-11-02 04:55:39 -0700 Implemented Kmer_search_end
src/kmer-search.c
src/kmer-search.h

2023-11-02 04:55:20 -0700 Added END method
src/method.c
src/method.h

2023-11-02 04:55:04 -0700 Implemented Path_solve_from_qstart and Path_solve_from_qend
src/path-solve.c
src/path-solve.h

2023-11-02 04:54:37 -0700 Path_solve_exact taking found_score as a parameter
src/path.c
src/path.h

2023-11-02 04:51:51 -0700 Using new interface to Trpath_solve_from_trstart and Trpath_solve_from_trend
src/transcriptome-search.c

2023-11-02 04:51:12 -0700 Getting trnum, troffset, and trhigh only after a successful extension
src/trpath-solve.c
src/trpath-solve.h

2023-11-02 04:50:11 -0700 Modified debugging statements
src/genomebits_trim.c

2023-11-01 13:34:19 -0700 Using new interface to Transcriptome_search_end
src/stage1hr-single.c

2023-11-01 13:34:06 -0700 Using new interfaces to Trpath_solve_from_trstart and Trpath_solve_from_trend
src/transcriptome-search.c
src/transcriptome-search.h

2023-11-01 13:33:39 -0700 Removed unused parameters from TR_END methods, and using Trpath_new_exact
src/trpath-solve.c
src/trpath-solve.h

2023-11-01 12:46:59 -0700 Moved trim procedures to genomebits_trim
src/genomebits_mismatches.c
src/genomebits_mismatches.h

2023-11-01 12:46:40 -0700 Calling Genomebits_trim procedure instead of Spliceends trim nosplice procedure, although the call is commented out
src/extension-search.c

2023-11-01 12:46:13 -0700 Added genomebits_trim
src/Makefile.dna.am
src/Makefile.gsnaptoo.am
src/gsnap.c

2023-11-01 12:44:56 -0700 Using Genomebits_trim procedures instead of Spliceends trim nosplice procedures
src/trpath-solve.c

2023-11-01 12:44:34 -0700 Using new interface to Spliceends trim nosplice procedures
src/splice.c

2023-11-01 12:43:40 -0700 Removed call to Genomebits_mismatches inside of Spliceends nosplice procedures, and expecting caller to perform it
src/spliceends.c
src/spliceends.h

2023-11-01 12:15:43 -0700 Moved Genomebits trim procedures from genomebits_mismatches.c to genomebits_trim.c
src/genomebits_trim.c
src/genomebits_trim.h

2023-11-01 10:30:47 -0700 Implemented trimming procedures that incorporate scoring from Spliceends nosplice procedures
src/genomebits_mismatches.c
src/genomebits_mismatches.h

2023-11-01 10:30:13 -0700 Added assertion checking for new Genomebits_trim procedures
src/spliceends.c

2023-11-01 10:29:48 -0700 Added typecasts to __m64
src/intersect-concordance-uint8.c

2023-11-01 10:28:13 -0700 Changed sscanf statement to use %llu instead of %lu
src/knownindels.c
src/knownsplicing.c

2023-11-01 10:27:44 -0700 Fixed print statement for large genomes
src/altsplice.c

2023-10-31 07:02:44 -0700 When merging paths, disallow attempt to find a microexon
src/stage3.c

2023-10-30 14:43:38 -0700 Removed references to intersect.h
src/kmer-search.c
src/segment-search.c

2023-10-30 14:35:21 -0700 Calling Uintlist_next instead of Univcoordlist_next
src/trpath-solve.c

2023-10-30 14:35:01 -0700 Fixed non-SIMD code
src/intersect-concordance-uint4.c

2023-10-30 14:34:50 -0700 Replaced unsigned int with Univcoord_T
src/intersect-concordance-uint8.h

2023-10-30 14:34:38 -0700 Using _mm256_set1_epi64x
src/intersect-concordance-uint8.c

2023-10-30 14:34:24 -0700 Replaced unsigned int with Univcoord_T
src/intersect-approx-uint8.c

2023-10-30 14:13:20 -0700 Enclosing Stage1_list_trpaths within a debugging macro
src/stage1hr.c

2023-10-30 14:13:01 -0700 Removed pass as a parameter
src/kmer-search.c
src/kmer-search.h

2023-10-30 14:12:47 -0700 In conversion procedures, exiting if the initial trstart is past the last exonbound
src/trpath-convert.c

2023-10-30 14:12:24 -0700 Implemented Trpath_solve_from_trstart and Trpath_solve_from_trend
src/trpath-solve.c
src/trpath-solve.h

2023-10-30 14:11:58 -0700 Implemented Transcriptome_search_end
src/transcriptome-search.c
src/transcriptome-search.h

2023-10-30 14:11:36 -0700 Implementing a flow for transcriptome methods to follow that for genome methods
src/stage1hr-paired.c

2023-10-30 14:10:47 -0700 Implemented a next_method procedure for transcriptome methods
src/stage1hr-single.h

2023-10-30 14:10:26 -0700 Implemented a next_method procedure for transcriptome methods
src/stage1hr-single.c

2023-10-30 14:10:00 -0700 In nosplice procedures, added potential code for resetting score to 0
src/spliceends.c

2023-10-30 14:09:31 -0700 Added method for TR_END
src/method.c
src/method.h

2023-10-30 14:09:12 -0700 Added comment
src/genomebits_mismatches.c

2023-10-30 14:09:05 -0700 Using new files for GSNAP and GSNAPL
src/Makefile.dna.am

2023-10-30 08:42:33 -0700 Performing a final extension in Trpath_solve_from_diagonals
src/trpath-solve.c

2023-10-30 08:42:01 -0700 Added comments
src/trpath.c

2023-10-30 08:41:43 -0700 Implemented Stage1_list_trpaths
src/stage1hr.c
src/stage1hr.h

2023-10-30 08:41:08 -0700 Rewrote order of search procedures in paired-end alignment, to have an initial search, then worst side to SEGMENT1, then both sides to SEGMENT1, then unextended search, and then anchored search
src/stage1hr-paired.c

2023-10-30 08:39:32 -0700 Checking distal end for completeness when finding a single-end fusion
src/stage1hr-single.c

2023-10-30 08:39:02 -0700 Not using presence of a fusion as a criterion for global cmp
src/pathpair-eval.c

2023-10-30 08:38:29 -0700 Fixed bug in Path_merge_genomichigh initializing with genomiclow.  Added checking functions for Path_fill and Path_merge procedures
src/path.c

2023-10-30 08:36:55 -0700 Using function Intlist_second_value
src/path-solve.c

2023-10-30 08:36:27 -0700 Fixed debugging statement
src/intersect-concordance-uint8.c

2023-10-30 08:35:47 -0700 Fixed debugging statement
src/intersect-concordance-uint4.c

2023-10-30 08:35:34 -0700 Removed pass as a parameter.  Changed debugging statements
src/extension-search.c
src/extension-search.h

2023-10-30 08:35:12 -0700 Added debugging statements
src/concordance.c

2023-10-29 09:59:35 -0700 Implemented paired_read_next_method, anchored_search, and unextended_search
src/stage1hr-paired.c

2023-10-29 09:59:04 -0700 Implemented single_read_next_method
src/stage1hr-single.c

2023-10-29 09:58:54 -0700 Implemented single_read_next_method
src/stage1hr-single.h

2023-10-29 09:33:30 -0700 Changed assertions
src/path-fusion.c

2023-10-29 09:33:21 -0700 Added METHOD_INIT
src/method.c
src/method.h

2023-10-29 09:33:05 -0700 Integrating complete paths from Path_extend into Stage1_T paths
src/concordance.c

2023-10-28 15:58:55 -0700 Removed temporary pointers
src/concordance.c

2023-10-28 15:50:30 -0700 Added intersect-concordance-uint4 and intersect-concordance-uint8
src/Makefile.gsnaptoo.am

2023-10-28 15:49:43 -0700 Added include of intersect-concordance-uint8
src/concordance.c
src/gsnap.c

2023-10-28 15:49:16 -0700 Changed type of indices from unsigned int to int
src/intersect-lower-small.c

2023-10-28 15:49:06 -0700 Using cmplt_epi64_mask
src/intersect-lower-large.c

2023-10-28 15:48:41 -0700 Using cmplt_epi64_mask
src/intersect-higher-large.c

2023-10-28 15:48:11 -0700 Changed type of indices from unsigned int to int.  Using cmplt_epi64_mask
src/intersect-higher-small.c

2023-10-28 15:47:30 -0700 Changed type of indices from unsigned int to int
src/intersect-concordance-uint4.c

2023-10-28 15:47:06 -0700 Initial import
src/intersect-concordance-uint8.c
src/intersect-concordance-uint8.h

2023-10-28 15:00:40 -0700 Calling Intersect_concordance_setup
src/gsnap.c

2023-10-28 15:00:29 -0700 Using new interface to Intersect_concordance
src/concordance.c

2023-10-28 15:00:08 -0700 Added an assertion to check that the path is in fwd direction
src/path-eval.c

2023-10-28 14:59:50 -0700 Restored previous code without worrying about extending paths
src/path-fusion.c
src/path-fusion.h

2023-10-28 14:57:37 -0700 Extending unextended paths before finding outer fusions
src/pathpair-eval.c
src/pathpair-eval.h

2023-10-28 14:57:16 -0700 Extending unextended paths before finding fusions
src/stage1hr-single.c
src/stage1hr-single.h

2023-10-28 14:56:54 -0700 Calling segment2 before handling unextended paths.  Using new interface to Concordance_gen
src/stage1hr-paired.c

2023-10-28 14:56:17 -0700 Added fields for storing unique coords and cumsums.  Implemented procedures for extending unextended paths and for flattening all paths
src/stage1hr.c
src/stage1hr.h

2023-10-28 14:55:16 -0700 Path fill and merge procedures now computing unique coordinates with cumsums.  Implemented Path_flatten_array
src/path.c
src/path.h

2023-10-28 14:53:53 -0700 Path_extend is now able to handle extend_qstart and extend_qend separately
src/path-solve.c
src/path-solve.h

2023-10-28 14:53:03 -0700 Using new interface to Path_solve_from_diagonals
src/extension-search.c
src/kmer-search.c
src/segment-search.c

2023-10-28 14:52:26 -0700 Fixed scalar_one_set function
src/intersect-approx-uint4.c
src/intersect-approx-uint8.c
src/intersect-higher-large.c
src/intersect-higher-small.c
src/intersect-lower-large.c
src/intersect-lower-small.c

2023-10-28 14:52:11 -0700 Fixed code to have different slop values on the negative and positive side for each set
src/intersect-concordance-uint4.c
src/intersect-concordance-uint4.h

2023-10-27 21:07:32 -0700 Using intersection procedures and de-duplicated coords
src/concordance.c
src/concordance.h

2023-10-27 21:07:03 -0700 Initial import
src/intersect-concordance-uint4.c
src/intersect-concordance-uint4.h

2023-10-27 14:35:07 -0700 Fixed debugging statements.  Backing up second index only when we reach npaths
src/concordance.c

2023-10-26 10:40:35 -0700 Put fusion code into separate procedures
src/path-fusion.c

2023-10-25 20:13:06 -0700 Added galloping search
src/concordance.c

2023-10-25 19:40:18 -0700 Advancing either pathsL or pathsH, whichever has fewer paths
src/concordance.c

2023-10-25 18:39:59 -0700 Path_merge procedures taking a new array already allocated.  Using memcpy to handle the tail part of the merge
src/path.c
src/path.h

2023-10-25 18:39:00 -0700 When mergep is true, making a single call to MALLOC, instead of two
src/concordance.c

2023-10-25 17:46:10 -0700 Implemented list_paths_array.  Commented out obsolete procedures
src/stage1hr.c
src/stage1hr.h

2023-10-25 17:45:49 -0700 Path_merge procedures now handling the case of zero paths
src/path.c

2023-10-25 17:45:22 -0700 Performing concordance based on either newpaths5 or newpaths3 being present, rather than both being present
src/concordance.c

2023-10-25 17:32:39 -0700 Using new Id tag
src/translation.c
src/translation.h
src/types.h
src/uint8table.c
src/uint8table.h
src/uint8table_rh.c
src/uint8table_rh.h
src/uint8tableuint.c
src/uinttable.c
src/uinttable.h
src/uinttable_rh.c
src/uinttable_rh.h
src/uinttableuint.c
src/uinttableuint.h
src/univdiag.h
src/univdiagdef.h
src/univinterval.c
src/univinterval.h

2023-10-25 16:05:16 -0700 Initializing lists to NULL
src/trpath-convert.c

2023-10-25 16:05:00 -0700 Storing final results as arrays of paths, rather than lists
src/stage1hr.c
src/stage1hr.h

2023-10-25 16:04:31 -0700 Using new interface to Concordance_gen
src/stage1hr-paired.c

2023-10-25 16:04:03 -0700 Keeping search results in local variables rather than Stage1_T fields
src/stage1hr-single.c

2023-10-25 16:03:12 -0700 Not calling Path_filter on existing arrays of paths
src/pathpair-eval.c

2023-10-25 16:02:59 -0700 Added code to handle arrays of paths
src/path.c
src/path.h

2023-10-25 16:02:40 -0700 Handling Stage1_T paths as arrays rather than lists
src/path-fusion.c

2023-10-25 16:02:02 -0700 Formatting changes
src/intersect-small.c

2023-10-25 16:01:51 -0700 Revised comment
src/intersect-large.c

2023-10-25 16:01:42 -0700 Cleaned up allocation code
src/intersect-approx-uint4.c
src/intersect-approx-uint8.c

2023-10-25 16:01:09 -0700 Handling old paths as a sorted array rather than a list, and merging if requested
src/concordance.c
src/concordance.h

2023-10-25 12:37:01 -0700 Storing and using existing extended_paths
src/concordance.c

2023-10-25 12:29:55 -0700 Added debugging code
src/path.c

2023-10-25 12:29:43 -0700 Calling Path_eval_nmatches on unextended paths before using them
src/stage1hr-paired.c

2023-10-25 12:29:16 -0700 Copying extended_paths when copying a path.  Calling Path_eval_nmatches in Path_fusion_inner procedures
src/path-fusion.c

2023-10-25 09:20:07 -0700 Using new interface to Path commands for extendedp and extended_paths
src/concordance.c
src/gsnap.c
src/path-eval.c
src/path-eval.h
src/path-fusion.c
src/path-fusion.h
src/path-solve.c
src/pathpair-eval.c
src/pathpair.c
src/pathpair.h
src/repair.c
src/repair.h
src/resulthr.c
src/resulthr.h
src/stage1hr-paired.c
src/stage1hr-single.c
src/stage1hr.c

2023-10-25 09:19:07 -0700 Initializing and freeing extendedp and extended_paths
src/path.c

2023-10-25 09:18:45 -0700 Added fields extendedp and extended_paths
src/path.h

2023-10-24 14:41:20 -0700 Using new filenames and procedure names
src/segment-search.c
src/segment-search.h

2023-10-24 14:41:00 -0700 Fixed compiler errors
src/intersect-approx-uint8.c
src/intersect-higher-large.c
src/intersect-higher-large.h
src/intersect-higher-small.c
src/intersect-higher-small.h
src/intersect-indices-large.c
src/intersect-indices-uint8.c
src/intersect-lower-large.c
src/intersect-lower-large.h
src/intersect-lower-small.c
src/intersect-lower-small.h

2023-10-24 14:40:29 -0700 Using new filenames
src/Makefile.gsnaptoo.am
src/gsnap.c

2023-10-24 13:52:01 -0700 Renamed files
src/intersect-higher-large.c
src/intersect-higher-large.h
src/intersect-higher-small.c
src/intersect-higher-small.h
src/intersect-large-approx-higher.c
src/intersect-large-approx-higher.h
src/intersect-large-approx-lower.c
src/intersect-large-approx-lower.h
src/intersect-lower-large.c
src/intersect-lower-large.h
src/intersect-lower-small.c
src/intersect-lower-small.h
src/intersect-uint4-approx-higher.c
src/intersect-uint4-approx-higher.h
src/intersect-uint4-approx-lower.c
src/intersect-uint4-approx-lower.h

2023-10-24 13:48:56 -0700 Using new procedure names
src/transcriptome-search.c

2023-10-24 13:48:40 -0700 Removed extraneous character
src/trpath-solve.c

2023-10-24 13:48:16 -0700 Calling movemask_pd instead of movemask_ps
src/intersect-large-approx-higher.c
src/intersect-large-approx-higher.h
src/intersect-large-approx-lower.c
src/intersect-large-approx-lower.h

2023-10-24 13:47:45 -0700 Moved setup procedure
src/intersect-uint4-approx-higher.c
src/intersect-uint4-approx-higher.h
src/intersect-uint4-approx-lower.c
src/intersect-uint4-approx-lower.h

2023-10-24 13:46:33 -0700 Added setup procedure
src/intersect-indices-large.c
src/intersect-indices-large.h
src/intersect-indices-uint8.c
src/intersect-indices-uint8.h

2023-10-24 13:42:03 -0700 Removed unused variables
src/intersect-indices-uint8.c
src/intersect-indices-uint8.h

2023-10-24 13:41:51 -0700 Fixed to return correct values for freq indices
src/intersect-indices-large.c
src/intersect-indices-large.h

2023-10-24 12:38:01 -0700 Renamed files
src/intersect-indices-small.c
src/intersect-indices-small.h
src/intersect-indices-uint4.c
src/intersect-indices-uint4.h

2023-10-24 12:31:15 -0700 Renamed files
src/intersect-indices-large.c
src/intersect-indices-large.h
src/intersect-large-indices.c
src/intersect-large-indices.h

2023-10-24 12:26:47 -0700 Renamed files
src/intersect-indices-uint4.c
src/intersect-indices-uint4.h
src/intersect-indices-uint8.c
src/intersect-indices-uint8.h
src/intersect-uint4-indices.c
src/intersect-uint4-indices.h
src/intersect-uint8-indices.c
src/intersect-uint8-indices.h

2023-10-24 12:25:36 -0700 Outputting correct values for freq index of the matching entry, rather than the start of each block
src/intersect-uint4-indices.c
src/intersect-uint4-indices.h
src/intersect-uint8-indices.c
src/intersect-uint8-indices.h

2023-10-24 12:24:34 -0700 Using new procedure names
src/kmer-search.c

2023-10-24 12:24:11 -0700 Moved procedures elsewhere
src/intersect.c
src/intersect.h

2023-10-24 12:23:48 -0700 Changed name of procedure
src/intersect-large.c
src/intersect-large.h

2023-10-24 12:22:12 -0700 Changed name of procedure
src/intersect-small.c
src/intersect-small.h

2023-10-24 12:21:57 -0700 Changed filenames
src/intersect-approx-uint4.c
src/intersect-approx-uint4.h
src/intersect-approx-uint8.c
src/intersect-approx-uint8.h

2023-10-24 12:18:09 -0700 Renamed files
src/intersect-approx-uint4.c
src/intersect-approx-uint4.h
src/intersect-approx-uint8.c
src/intersect-approx-uint8.h
src/intersect-uint4-approx.c
src/intersect-uint4-approx.h
src/intersect-uint8-approx.c
src/intersect-uint8-approx.h

2023-10-24 12:16:42 -0700 Changed function name
src/intersect-uint4-approx.c
src/intersect-uint4-approx.h

2023-10-24 12:15:45 -0700 Initial import
src/intersect-uint8-approx.c
src/intersect-uint8-approx.h

2023-10-24 12:03:28 -0700 Renamed files
src/intersect-small.c
src/intersect-small.h
src/intersect-uint4.c
src/intersect-uint4.h

2023-10-24 11:59:50 -0700 Declaring a variable for the non-SIMD code
src/intersect-uint2.c

2023-10-24 11:59:16 -0700 Checking for both HAVE_SSE4_1 and HAVE_MM_EXTRACT_EPI64
src/genomebits.h

2023-10-23 19:08:35 -0700 Renamed files
src/intersect-large-approx-higher.c
src/intersect-large-approx-higher.h
src/intersect-large-approx-lower.c
src/intersect-large-approx-lower.h
src/intersect-uint8-approx-higher.c
src/intersect-uint8-approx-higher.h
src/intersect-uint8-approx-lower.c
src/intersect-uint8-approx-lower.h

2023-10-23 19:06:14 -0700 Initial import
src/intersect-uint8-approx-higher.c
src/intersect-uint8-approx-higher.h
src/intersect-uint8-approx-lower.c
src/intersect-uint8-approx-lower.h

2023-10-23 19:05:39 -0700 Initial import
src/intersect-uint4-indices.c
src/intersect-uint4-indices.h

2023-10-23 19:05:09 -0700 Removed parameters for first_p
src/intersect-large-indices.c
src/intersect-large-indices.h

2023-10-23 19:04:41 -0700 Allowing compilation for SSE2
src/intersect-uint2.c

2023-10-23 19:04:27 -0700 Various changes
src/intersect-uint4-approx-higher.c
src/intersect-uint4-approx-higher.h
src/intersect-uint4-approx-lower.c
src/intersect-uint4-approx-lower.h

2023-10-23 19:03:37 -0700 Using LOAD_SI128 macro
src/intersect-uint4-approx.c
src/intersect-uint4-approx.h

2023-10-23 19:03:02 -0700 Various changes
src/intersect-uint4.c

2023-10-23 18:59:23 -0700 Renamed files
src/intersect-large.c
src/intersect-large.h
src/intersect-uint8.c
src/intersect-uint8.h

2023-10-23 18:58:17 -0700 Initial import
src/intersect-uint8.c
src/intersect-uint8.h

2023-10-23 18:58:00 -0700 Renamed files
src/intersect-large.c
src/intersect-large.h
src/intersect-large.old.c
src/intersect-large.old.h

2023-10-23 18:56:56 -0700 Removed non-SIMD code
src/intersect-large.c
src/intersect-large.h

2023-10-23 18:54:31 -0700 Initial import
src/intersect-uint8-indices.c
src/intersect-uint8-indices.h

2023-10-23 18:04:09 -0700 Renamed files
src/intersect-large-indices.c
src/intersect-large-indices.h
src/intersect-uint8-indices.c
src/intersect-uint8-indices.h

2023-10-23 18:03:04 -0700 Initial import
src/intersect-uint8-indices.c
src/intersect-uint8-indices.h

2023-10-23 12:24:56 -0700 Renamed files
src/intersect-approx-simd.c
src/intersect-approx-simd.h
src/intersect-uint4-approx.c
src/intersect-uint4-approx.h

2023-10-23 09:47:33 -0700 Renamed files
src/intersect-approx-higher.c
src/intersect-approx-higher.h
src/intersect-approx-lower.c
src/intersect-approx-lower.h
src/intersect-uint4-approx-higher.c
src/intersect-uint4-approx-higher.h
src/intersect-uint4-approx-lower.c
src/intersect-uint4-approx-lower.h

2023-10-23 08:52:41 -0700 Implemented AVX512 version of v3 and fixed AVX2 version.  In v1, eliminated duplicate loading of freq when advancing rare.
src/intersect-uint4.c

2023-10-22 19:25:00 -0700 Renamed intersect-simd.c to intersect-uint4.c
src/Makefile.gsnaptoo.am
src/intersect-simd.c
src/intersect-simd.h
src/intersect-uint4.c
src/intersect-uint4.h
src/kmer-search.c
src/localdb-read.c
src/transcriptome-search.c

2023-10-22 19:15:56 -0700 Implemented SIMD using AVX512
src/intersect-approx-higher.c
src/intersect-approx-lower.c
src/intersect-approx-simd.c
src/intersect-simd.c

2023-10-22 17:22:54 -0700 Updated version number
VERSION
config.site.rosalind.prd

2023-10-22 17:21:12 -0700 Made single-end procedures follow the flow for paired-end reads
src/stage1hr-single.c
src/stage1hr-single.h

2023-10-22 17:20:14 -0700 In anchored search, trying worse side and then both sides.  Using new interfaces to search procedures without found_transcriptp as parameter.  Using new interface to procedures from stage1hr-single.c.
src/stage1hr-paired.c

2023-10-22 17:16:10 -0700 Added back fields for sense_trpaths and antisense_trpaths
src/stage1hr.c
src/stage1hr.h

2023-10-22 17:15:46 -0700 Copying tr_endpoints and tr_nmismatches, so that a subsequent conversion will work
src/trpath-convert.c

2023-10-22 17:15:10 -0700 Implemented Trpath_eval_nmatches for debugging
src/trpath-solve.c
src/trpath-solve.h

2023-10-22 17:14:32 -0700 Implemented Trpath_trnum_cmp
src/trpath.c
src/trpath.h

2023-10-22 17:14:04 -0700 Added assertion
src/splice.c

2023-10-22 17:13:53 -0700 Implemented procedures for Path_trnum_low and Path_trnum_high
src/path.c
src/path.h

2023-10-22 17:13:12 -0700 Using new interface to Transcript_remap_all
src/path-fusion.c

2023-10-22 17:12:57 -0700 Implemented Concordance_tr
src/concordance.c
src/concordance.h

2023-10-22 17:12:11 -0700 No longer returning found_transcriptp
src/path-solve.c
src/path-solve.h

2023-10-22 17:11:26 -0700 No longer returning found_transcriptp
src/transcript-remap.c
src/transcript-remap.h

2023-10-22 17:10:39 -0700 No longer returning found_transcriptp
src/extension-search.c
src/extension-search.h
src/kmer-search.c
src/kmer-search.h
src/segment-search.c
src/segment-search.h
src/tr-extension-search.c
src/tr-extension-search.h
src/transcriptome-search.c
src/transcriptome-search.h

2023-10-22 10:28:54 -0700 Re-wrote steps for TR, RNA, and DNA tasks to try worse side first and then both sides for each method
src/stage1hr-paired.c

2023-10-20 11:15:51 -0700 Moving transcript concordance to be of lesser importance than nmatches
src/pathpair-eval.c
src/pathpair-eval.h

2023-10-20 11:15:19 -0700 Implemented Path_check_valid
src/path.c
src/path.h

2023-10-20 11:14:55 -0700 Removed faulty assertion
src/path-solve.c

2023-10-20 11:14:44 -0700 Making use of value for --sam-use-0M
src/path-print-sam.c
src/path-print-sam.h

2023-10-20 11:14:20 -0700 Added an assertion that each nmismatches must be >= 0
src/path-eval.c

2023-10-20 11:14:01 -0700 Consolidated methods from TR, RNA, and DNA tasks
src/method.c
src/method.h

2023-10-20 11:13:23 -0700 Added steps for transcriptome-guided alignment.  Calling concordance multiple times
src/stage1hr-paired.c

2023-10-20 11:12:45 -0700 Search procedures provide lists of paths as outputs, rather than modifying Stage1_T object, so we can run concordance multiple times
src/stage1hr-single.c
src/stage1hr-single.h

2023-10-20 11:11:38 -0700 Removed fields for trpaths.  Added fields for exact_univdiagonals
src/stage1hr.c
src/stage1hr.h

2023-10-20 11:07:01 -0700 Conversion procedures call Path_eval_nmatches
src/trpath-convert.c
src/trpath-convert.h

2023-10-20 11:06:33 -0700 Computing counts when finding most prevalent diagonals
src/transcriptome-search.c

2023-10-20 11:05:53 -0700 Computing counts when determining most prevalent diagonals
src/kmer-search.c

2023-10-20 11:05:30 -0700 Formatting changes
src/intersect-simd.c

2023-10-20 11:05:19 -0700 Added an argument to --sam-use-0M flag.  Calling setup procedures for new Intersect_approx procedures
src/gsnap.c

2023-10-20 10:16:53 -0700 Moved Intersect_approx_lower and Intersect_approx_higher code to intersect-approx-lower.c and intersect-approx-higher.c
src/intersect.c
src/intersect.h

2023-10-20 10:16:05 -0700 Checking for freq < stopFreq before reading in a vector
src/intersect-approx-simd.c

2023-10-20 10:14:42 -0700 Performing Path_filter on new paths
src/concordance.c
src/concordance.h

2023-10-20 10:13:47 -0700 Implemented SIMD versions of Intersect_approx_lower and Intersect_approx_higher
src/Makefile.gsnaptoo.am
src/intersect-approx-higher.c
src/intersect-approx-higher.h
src/intersect-approx-lower.c
src/intersect-approx-lower.h

2023-10-13 18:02:53 -0700 Fixed Path_solve_junctions to handle indels as well as splices
src/path-solve.c

2023-10-13 13:42:08 -0700 Using new interface to Shortread_print_chopped_end_quality and Shortread_print_chopped_end_quality_reverse
src/path-print-sam.c

2023-10-13 13:41:36 -0700 Fixed hardclipped print routines for quality strings
src/shortread.c
src/shortread.h

2023-10-11 11:18:25 -0700 Updated version number
VERSION
config.site.rosalind.prd
config.site.rosalind.tst
share/index.html

2023-10-10 06:33:52 -0700 Printing hardclipped regions together with poly-A regions
src/shortread.c

2023-10-04 10:19:14 -0700 Updated version number
VERSION
config.site.rosalind.prd
config.site.rosalind.tst

2023-10-02 08:13:30 -0700 Handling failedinput better
src/path-print-sam.c
src/path-print-sam.h

2023-10-02 08:12:28 -0700 Made Output_setup compatible with gmap
src/gsnap.c
src/output.c
src/output.h

2023-09-29 16:40:14 -0700 Added option --only-tr-consistent
src/gsnap.c

2023-09-29 16:39:54 -0700 Distinguishing between x and y for cryptic splice sites
src/trpath-convert.c

2023-09-29 16:39:38 -0700 Modified debugging statements
src/transcript.c

2023-09-29 16:39:24 -0700 Fixed issue with firstchar being based on the wrong test.  Distinguishing between x and y for cryptic splice sites
src/transcript-remap.c

2023-09-29 16:38:15 -0700 Added field tr_consistent_p
src/resulthr.c
src/resulthr.h

2023-09-29 16:38:02 -0700 Added tr_consistent_p.  Not printing invalid transcript if valid ones exist
src/path-print-sam.c
src/path-print-sam.h

2023-09-29 16:37:29 -0700 Added tr_consistent_p
src/output.c
src/output.h

2023-09-29 16:36:56 -0700 Using Id tag
src/outbuffer.c
src/outbuffer.h

2023-09-28 08:45:55 -0700 In computing MD strings, not advancing pointer p by choplength
src/path-print-sam.c

2023-09-27 09:31:23 -0700 Reverting back to not separating suboptimal trpaths
src/stage1hr-paired.c
src/stage1hr-single.c
src/stage1hr.c
src/stage1hr.h

2023-09-27 09:30:43 -0700 Calling Genome_mark_mismatches if the query sequence has a non-ACGT character
src/path-eval.c

2023-09-27 09:30:08 -0700 Implemented Compress_non_acgt
src/compress.c
src/compress.h

2023-09-27 09:29:49 -0700 For typical call to mark_mismatches, setting query_unk_mismatch_p and genome_unk_mismatch_p to be true.  Added separate debugging statements for mark_mismatches
src/genomebits_count.c

2023-09-27 07:43:28 -0700 Changed type of nmatches and querylength from UINT4 to int, because of problem with short querylengths
src/sarray-read.c
src/sarray-read.h

2023-09-26 21:39:50 -0700 Implemented Trpath_filter_best
src/trpath.c
src/trpath.h

2023-09-26 19:06:03 -0700 Using new interfaces to transcriptome methods
src/stage1hr-paired.c

2023-09-26 19:05:28 -0700 Cleaned up code for transcriptome-guided search.  Removed segment1 method from transcriptome-guided search
src/stage1hr-single.c

2023-09-26 19:04:42 -0700 Added fields for lists of Trpath_T objects
src/stage1hr.c
src/stage1hr.h

2023-09-26 19:04:18 -0700 Modifying lists for Trpath_T objects instead of those for Path_T objects
src/transcriptome-search.c
src/transcriptome-search.h

2023-09-26 19:03:32 -0700 Turned off localdb for DNA-seq.  Calling Trpath_setup and Trpath_convert_setup
src/gsnap.c

2023-09-26 19:02:42 -0700 Added trpath-convert
src/Makefile.dna.am
src/Makefile.gsnaptoo.am

2023-09-26 19:02:30 -0700 Moved code from trpath.c to trpath-convert.c
src/trpath.c
src/trpath.h

2023-09-26 19:01:59 -0700 Moved code from trpath.c to trpath-convert.c
src/trpath-convert.c
src/trpath-convert.h

2023-09-26 19:01:31 -0700 Returning Trpath_T objects instead of converting immediately to Path_T objects
src/trpath-solve.c
src/trpath-solve.h

2023-09-26 19:00:16 -0700 Returning Trpath_T objects instead of converting immediately to Path_T objects
src/tr-extension-search.c
src/tr-extension-search.h

2023-09-26 18:59:12 -0700 Renamed Path_create_simple to Path_convert_simple
src/path.c
src/path.h

2023-09-26 18:58:34 -0700 Kmer_search_complete providing correct parameters to Path_solve_from_diagonals
src/kmer-search.c

2023-09-26 13:25:11 -0700 Fixed incorrect variable in previous patch
src/path-print-sam.c

2023-09-26 08:37:08 -0700 For printing hardclipped sequences, accounting for hardclips including the chopped sequence on the same side
src/shortread.c

2023-09-26 08:36:22 -0700 Fixed CIGAR strings for chopped sequence plus hardclip
src/path-print-sam.c

2023-09-26 08:35:43 -0700 Fixed endpoints to Splice_resolve when previous junction is an insertion
src/path-solve.c

2023-09-26 08:34:55 -0700 Added comment
src/path-eval.c

2023-09-22 11:37:42 -0700 Created separate procedures for transcriptome-guided, RNA, and DNA tasks
src/stage1hr-paired.c
src/stage1hr-single.c
src/stage1hr-single.h

2023-09-22 11:37:10 -0700 Added code for Kmer_search_complete.  Taking method as a parameter
src/kmer-search.c
src/kmer-search.h

2023-09-22 11:36:24 -0700 Taking method as a parameter
src/extension-search.c
src/extension-search.h

2023-09-22 11:36:01 -0700 Changed UINT4 to Trcoord_T.  Using correct tr oligos
src/transcriptome-search.c

2023-09-22 11:35:17 -0700 Added the fields all_oligos_gen_filledp and all_positions_gen_filledp
src/stage1hr.c
src/stage1hr.h

2023-09-22 11:34:40 -0700 Created different sets of methods for different alignment tasks, so they can be re-ordered independently
src/method.c
src/method.h

2023-09-20 13:40:01 -0700 No longer printing paired ends under --quiet-if-excessive --nofails
src/path-print-sam.c

2023-09-20 13:16:28 -0700 In Path_solve_junctions, advancing endpoint pointer correctly after a splice with indel.  Added assertions
src/path-solve.c

2023-09-19 23:35:39 -0700 Reducing the size of localdb_alloc
src/stage1hr-paired.c
src/stage1hr-single.c

2023-09-19 23:35:26 -0700 Using localdb_alloc only for the result, not the short set
src/intersect-uint2.c

2023-09-19 23:29:38 -0700 Rewrote code for transcript remap procedures
src/transcript-remap.c

2023-09-19 23:29:09 -0700 Modified debugging statements
src/splice.c

2023-09-19 23:28:47 -0700 In Path_solve_junctions with a middle_univdiagonal, setting the two splice_qpos values in the correct order
src/path-solve.c

2023-09-19 23:27:54 -0700 Fixed code for non-STTNI vector intersection.  No longer copying memory, but performing scalar intersection until we reach an aligned pointer
src/intersect-uint2.c

2023-09-19 12:19:38 -0700 Restored non-SIMD binaries
src/Makefile.dna.am
src/Makefile.gsnaptoo.am

2023-09-19 12:19:22 -0700 Revised comment
src/transcript-remap.c

2023-09-19 12:14:58 -0700 Not trimming trstart or trend when final splice site is cryptic
src/transcript.c

2023-09-19 12:13:41 -0700 Using non-SIMD version of Intersect_uint2 when appropriate
src/localdb-read.c

2023-09-19 12:13:08 -0700 Fixed bug from using wrong diagterm.  Fixed missing intersections from underflow or overflow of unsigned short.  Implemented non-SIMD version
src/intersect-uint2.c
src/intersect-uint2.h

2023-09-19 12:07:47 -0700 Fixed non-SIMD code
src/intersect-approx-simd.c

2023-09-19 12:07:20 -0700 Allowing for non-SIMD program
src/genomebits.c
src/genomebits_consec.c

2023-09-18 18:45:49 -0700 Modified debugging statements
src/transcript.c

2023-09-18 18:45:28 -0700 In Transcript_remap_geneplus, when alignment starts before an exon, using the previous exonbound
src/transcript-remap.c

2023-09-18 18:44:37 -0700 Providing parameter to free transcripts
src/repair.c
src/repair.h

2023-09-18 18:43:09 -0700 Using Intlist_second_value.  Using new interface to Repair_free
src/path-solve.c

2023-09-18 08:41:18 -0700 Fixed calculation of qend in Path_solve_junctions
src/path-solve.c

2023-09-16 09:45:22 -0700 Fixed the check for reallocation to account for the writing of two diagonals per diagpair
src/intersect-approx-simd.c

2023-09-14 21:58:03 -0700 In approximate search, handling the output of Intersect_approx, which can include exact matches.  For each group of diagpairs, picking the pair with the smallest distance
src/transcriptome-search.c

2023-09-14 21:56:46 -0700 In Path_qstart_resolve and Path_qend_resolve, checking for a possible insertion.  In adding splices at qstart or qend, checking if distal univdiagonal is the same as medial univdiagonal
src/path-solve.c

2023-09-14 21:55:40 -0700 Turned on INCLUDE_EXACT and fixed code for that case
src/intersect-approx-simd.c

2023-09-14 12:54:29 -0700 Added galloping search to v1 algorithm
src/intersect-approx-simd.c

2023-09-14 12:17:31 -0700 Removed old debugging statements
src/transcriptome-search.c

2023-09-14 12:17:15 -0700 Fixed reallocation code
src/intersect-approx-simd.c

2023-09-13 23:37:36 -0700 Using listpool and intlistpool in Path_consolidate
src/path-eval.c

2023-09-13 23:00:11 -0700 Updated version number
VERSION
config.site.rosalind.prd
config.site.rosalind.tst

2023-09-13 22:59:52 -0700 Formatting change
configure.ac

2023-09-13 22:58:33 -0700 Added criteria to Path_common_structure_p: common univdiagonal needs to be the longest for each path, the number of leading and trailing univdiagonals cannot exceed 1, and there cannot be a crossover of leading and trailing univdiagonals
src/path.c

2023-09-13 21:11:11 -0700 In Path_common_structure_p, added a check for mismatched leading and trailing univdiagonals
src/path.c

2023-09-13 21:10:42 -0700 Formatting change
src/path-eval.c

2023-09-13 20:57:57 -0700 Modified debugging statement
src/trpath.c

2023-09-13 20:57:44 -0700 Added debugging statement
src/transcript.c

2023-09-13 20:57:34 -0700 Added debugging code
src/transcript-velocity.c

2023-09-13 20:56:30 -0700 Using new interface to Path_consolidate
src/stage1hr-paired.c
src/stage1hr-single.c
src/stage1hr.c
src/stage1hr.h

2023-09-13 20:56:10 -0700 Assigning an uninitialized variable
src/path-trim.c

2023-09-13 20:55:59 -0700 In Path_solve_junctions, using Transcript_remap_invalid instead of previous code
src/path-solve.c

2023-09-13 20:55:12 -0700 Using new procedure name Transcript_remap_all
src/path-fusion.c

2023-09-13 20:54:58 -0700 Computing transcript_chrnum_crosstable and providing it to transcript remap procedures
src/gsnap.c

2023-09-13 20:53:45 -0700 Fixed issue where chromosome order in map IIT can be different from that in chromosome IIT.  Implemented Transcript_remap_invalid
src/transcript-remap.c
src/transcript-remap.h

2023-09-13 20:52:52 -0700 In Path_consolidate, processing invalid transcripts through Transcript_remap_invalid
src/path-eval.c
src/path-eval.h

2023-09-13 20:51:00 -0700 Updated Id tag
src/iit-read-univ.c

2023-09-13 20:50:32 -0700 Added comment about chromosome order in genes iit being different from that in chromosome iit
util/gmap_build.pl.in

2023-09-13 19:51:01 -0700 Fixed memory leak of diagonals returned from Intersect_approx
src/transcriptome-search.c

2023-09-12 19:29:58 -0700 Fixed Hitlist_push into the wrong list
src/path-solve.c

2023-09-12 19:29:31 -0700 Fixed memory leaks of Trpath_T objects
src/trpath-solve.c

2023-09-12 19:01:29 -0700 Renamed a variable
src/pathpair.c

2023-09-12 19:01:15 -0700 Added option --resolve-inner to control resolving soft-clipping on the insides of paired-end reads.  Restored --pairexpect and --pairdev to the help output
src/gsnap.c
src/pathpair-eval.c
src/pathpair-eval.h

2023-09-12 18:14:22 -0700 Added potential code to perform segment2 method using unextended paths
src/stage1hr-paired.c

2023-09-12 18:13:32 -0700 Restored segment1 method in transcriptome-guided alignment
src/stage1hr-single.c

2023-09-12 18:13:06 -0700 Renamed parameter from nmismatches_allowed to localdb_nmismatches_allowed
src/spliceends.c
src/spliceends.h

2023-09-12 18:12:41 -0700 Removed unsolved_paths as parameters
src/segment-search.c
src/segment-search.h

2023-09-12 18:12:22 -0700 Implemented Pathpair_found_score
src/pathpair.h

2023-09-12 18:12:08 -0700 Renamed parameter from nmismatches_allowed to localdb_nmismatches_allowed
src/path-solve.h

2023-09-12 18:11:44 -0700 No longer filtering reads into unsolved if more than 8 bp remains at the end, which misses the chance to combine qstart and qend paths
src/path-solve.c

2023-09-12 18:08:34 -0700 No longer calling Stage1hr_paired_read a second time with chopped primers
src/gsnap.c

2023-09-12 18:07:38 -0700 Concordance_simple now returning found_score_paired
src/concordance.c
src/concordance.h

2023-09-12 14:59:29 -0700 Fixed uninitialized variable
src/trpath.c

2023-09-12 14:59:14 -0700 Simplified code in Transcript_remap_geneplus and Transcript_remap_geneminus to assume exoni <= exonj
src/transcript-remap.c

2023-09-12 14:57:51 -0700 Removed comment
src/stage1hr-single.c

2023-09-12 14:57:32 -0700 Added debugging statements
src/path-solve.c

2023-09-12 14:57:09 -0700 Having separate equivalence classes for transcriptome and non-transcriptome methods
src/path-eval.c

2023-09-12 12:01:05 -0700 Added include of uintlistpool.h
src/stage1hr.h

2023-09-12 11:27:11 -0700 Added intersect-approx-simd
src/Makefile.dna.am

2023-09-12 11:16:46 -0700 Updated version number
config.site.rosalind.prd

2023-09-12 11:16:44 -0700 Updated version number
config.site.rosalind.tst

2023-09-12 11:16:35 -0700 Updated version number
VERSION

2023-09-12 10:59:39 -0700 Added intersect-approx-simd
src/Makefile.gsnaptoo.am

2023-09-12 10:59:22 -0700 Making sure to call Path_consolidate before returning paths.  Using new Stage1 procedures for solving unsolved paths and consolidating paths
src/stage1hr-paired.c
src/stage1hr-single.c
src/stage1hr-single.h

2023-09-12 10:58:30 -0700 Implemented Stage1_solve_unsolved_paths and Stage1_consolidate_paths
src/stage1hr.c
src/stage1hr.h

2023-09-12 10:58:00 -0700 Commented out unused procedure
src/trpath-solve.c

2023-09-12 10:57:51 -0700 Modified debugging statements
src/trpath.c

2023-09-12 10:57:36 -0700 Removed nmismatches_allowed as a parameter to Transcriptome_search_complete
src/transcriptome-search.c
src/transcriptome-search.h

2023-09-12 10:57:10 -0700 Added assertion for trstart < trend
src/transcript.c

2023-09-12 10:56:55 -0700 Checking for exons being entirely within an intron
src/transcript-remap.c
src/transcript-remap.h

2023-09-12 10:56:18 -0700 Using new interface to Transcript_remap
src/path-fusion.c

2023-09-12 10:55:54 -0700 Using new interface to Path_solve_from_ends
src/kmer-search.c
src/kmer-search.h

2023-09-12 10:55:30 -0700 Calling Repair_setup
src/gsnap.c

2023-09-12 10:55:17 -0700 Repair_path now checking for nmismatches and adequate support at distal segment
src/repair.c
src/repair.h

2023-09-12 10:54:24 -0700 Removed parameter nmismatches_allowed from Path_solve_from_ends
src/path-solve.c
src/path-solve.h

2023-09-12 10:49:20 -0700 Using new interface to Repair_path.  Path_solve_from_ends no longer checking against nmismatches_allowed
src/path-solve.c

2023-09-12 10:47:45 -0700 Edited comment
src/path.h

2023-09-12 10:47:36 -0700 Checking whether trims are longer than Path_coverage
src/path.c

2023-09-12 10:47:13 -0700 Checking that trims are compatible when creating equivalence classes
src/path-eval.c
src/path-eval.h

2023-09-12 10:46:24 -0700 Moved Intersect_approx to intersect-approx-simd.c
src/intersect.c

2023-09-12 10:45:51 -0700 Fixed code used for checking SIMD vs non-SIMD
src/intersect-simd.c
src/intersect-simd.h

2023-09-11 18:33:22 -0700 Using spliceends procedure to determine region for splice_qpos
src/splice.c
src/splice.h

2023-09-11 18:32:49 -0700 Removed unused parameters
src/extension-search.c
src/extension-search.h
src/kmer-search.c
src/kmer-search.h
src/path-solve.c
src/path-solve.h
src/repair.c
src/repair.h
src/segment-search.c
src/stage1hr-paired.c
src/stage1hr-single.c
src/stage1hr-single.h
src/tr-extension-search.c
src/tr-extension-search.h
src/transcriptome-search.c
src/transcriptome-search.h
src/trpath-solve.c
src/trpath-solve.h
src/trpath.c

2023-09-11 15:44:40 -0700 When assertions are checked, printing transcript nums
src/transcript.c

2023-09-11 15:44:19 -0700 Modified comment
src/transcript.h

2023-09-11 15:44:00 -0700 Making some remapping procedures available externally
src/transcript-remap.c
src/transcript-remap.h

2023-09-11 15:42:59 -0700 Using new interfaces to Trpath_solve procedures
src/tr-extension-search.c
src/tr-extension-search.h

2023-09-11 15:42:38 -0700 Using new interfaces to Trpath_solve procedures
src/transcriptome-search.c
src/transcriptome-search.h

2023-09-11 15:41:46 -0700 Using new interface to conversion procedures to save unsolved paths
src/trpath-solve.c
src/trpath-solve.h

2023-09-11 15:41:23 -0700 Storing alignments with indel/splice to a list of unsolved paths
src/trpath.c
src/trpath.h

2023-09-11 15:40:24 -0700 Using new interfaces to transcriptome methods.  Calling Path_solve_junctions
src/stage1hr-paired.c

2023-09-11 15:39:55 -0700 Added procedures for calling Path_consolidate and Path_solve_junctions on all four sensedir and plusp lists
src/stage1hr-single.c
src/stage1hr-single.h

2023-09-11 15:39:01 -0700 Added function Stage1_dump_tr
src/stage1hr.c
src/stage1hr.h

2023-09-11 15:38:42 -0700 In Path_solve_junctions, modifying the invalid transcript
src/path-solve.h

2023-09-11 15:38:18 -0700 In Path_solve_junctions, modifying the invalid transcript
src/path-solve.c

2023-09-11 15:37:52 -0700 In Path_consolidate, accumulating invalid transcripts
src/path-eval.c

2023-09-11 15:37:00 -0700 In standard mode, assigning character conversions for +1 and -1 genestrands
src/oligo.c
src/oligo.h

2023-09-11 15:36:03 -0700 Added include for string.h
src/intersect-approx-simd.c

2023-09-11 15:35:49 -0700 Calling setup for Intersect_approx
src/gsnap.c

2023-09-11 15:08:23 -0700 Fixed SIMD code
src/intersect-approx-simd.c

2023-09-11 06:10:27 -0700 Initial implementation
src/intersect-approx-simd.c
src/intersect-approx-simd.h

2023-09-09 10:05:01 -0700 Added debugging code
src/exon.c

2023-09-09 10:04:33 -0700 Using new interfaces to transcriptome methods
src/stage1hr-paired.c
src/stage1hr-single.c

2023-09-09 10:04:14 -0700 Added new parameters for transcriptome methods
src/tr-extension-search.c
src/tr-extension-search.h

2023-09-09 10:03:54 -0700 Added new parameters for transcriptome methods
src/transcriptome-search.c
src/transcriptome-search.h

2023-09-09 10:03:11 -0700 Using new interfaces to conversion procedures
src/trpath-solve.c
src/trpath-solve.h

2023-09-09 10:02:42 -0700 In conversion procedures, for indels next to splices, now using unsolved junctions and calling Path_solve_junctions
src/trpath.c
src/trpath.h

2023-09-09 10:01:28 -0700 Changed Path_create_from_transcripts to Path_create_simple
src/path.c
src/path.h

2023-09-09 10:01:07 -0700 Made Path_solve_junctions work again
src/path-solve.c
src/path-solve.h

2023-09-09 09:59:59 -0700 Added potential code if we allowed invalid transcripts from transcriptome methods
src/path-eval.c

2023-09-08 18:18:58 -0700 Added code in conversion procedures to merge indels adjacent to splice sites
src/trpath.c

2023-09-08 16:30:48 -0700 Computing exons within conversion procedures
src/trpath.c

2023-09-08 00:05:34 -0700 Formatting change
src/path.h

2023-09-08 00:05:14 -0700 Initialized variables
src/path-trim.c

2023-09-08 00:04:58 -0700 Revised Path_consolidate to identify equivalence classes within each group of overlapping paths
src/path-eval.c

2023-09-08 00:04:19 -0700 Improved algorithm for Path_common_structure_p to compute based on a sequence of common univdiagonals
src/path.c

2023-09-06 22:28:45 -0700 Merge branch 'main' of ssh.code.roche.com:/twu/gmap into main
2023-09-06 22:26:17 -0700 Using new interface to Path_consolidate
src/stage1hr-single.c

2023-09-06 22:25:40 -0700 In conversion procedures, changing deletionpos to a genomic coordinate
src/trpath.c

2023-09-06 22:25:11 -0700 Using new interface to Path_trim procedures
src/path-eval.c
src/path-eval.h

2023-09-06 22:24:52 -0700 For Path_trim_qstart_n and Path_trim_qend_n, making a call to Path_eval_nmatches
src/path-trim.c
src/path-trim.h

2023-09-06 20:22:35 -0700 Using new interface to Stage1hr_paired_setup
src/gsnap.c

2023-09-06 20:22:22 -0700 Filling all positions for genomic in segment2 method when transcriptome_align_p is true
src/stage1hr-paired.c
src/stage1hr-paired.h

2023-09-06 20:19:17 -0700 No longer calling segment1 when transcriptome_align_p is true
src/stage1hr-single.c

2023-09-06 20:18:54 -0700 Fixed incorrect handling of result from Path_eval_nmatches.  No longer removing reads based on nmismatches_allowed
src/trpath-solve.c

2023-09-06 20:17:43 -0700 Separating retrievedp for genome and transcriptome
src/stage1hr.c

2023-09-06 20:16:58 -0700 No longer removing path based on nmismatches_allowed
src/path-solve.c

2023-09-06 20:16:30 -0700 Added comment
src/path-eval.c

2023-09-06 19:49:59 -0700 Using new interfaces to Stage1hr oligo and position procedures
src/stage1hr-paired.c
src/stage1hr-single.c

2023-09-06 19:49:21 -0700 Removed queryuc_ptr as a parameter to Stage1hr oligo and position procedures
src/stage1hr.c
src/stage1hr.h

2023-09-06 19:45:00 -0700 Modified debugging statement
src/segment-search.c

2023-09-06 19:44:16 -0700 Modified debugging statement
src/kmer-search.c

2023-09-06 18:26:15 -0700 Not performing Path_extend on paths from transcriptome methods.  Using new interfaces to transcriptome search procedures
src/stage1hr-paired.c

2023-09-06 18:25:48 -0700 Using new interfaces to transcriptome search procedures
src/stage1hr-single.c

2023-09-06 18:25:27 -0700 Fixed computation of exonj when alignment hits the end of the exon.  Providing Transcript_new with 1-based coordinates
src/trpath.c

2023-09-06 18:24:09 -0700 For paths from transcriptome methods, putting results into fully extended results
src/tr-extension-search.c
src/tr-extension-search.h
src/transcriptome-search.c
src/transcriptome-search.h

2023-09-06 18:23:25 -0700 Added assertion to Path_extend that transcriptome_method_p is false
src/path-solve.c

2023-09-06 18:22:50 -0700 In Path_consolidate, transferring all transcripts from eliminated paths to bestpath
src/path-eval.c

2023-09-06 18:22:04 -0700 Fixed computation of nsegments and remainder for Path_trim_qstart_n and Path_trim_qend_n
src/path-trim.c

2023-09-06 18:21:39 -0700 Assigning transcriptome_method_p.  Path_unextendedp is false for transcriptome methods
src/path.c

2023-09-06 18:21:04 -0700 Added a field transcriptome_method_p
src/path.h

2023-09-06 15:18:09 -0700 Adding reader and tr_reader as fields in Stage1_T object
src/stage1hr.c
src/stage1hr.h

2023-09-06 15:17:47 -0700 Re-ordered methods for speed.  Turning off some methods when transcriptome is available
src/stage1hr-paired.c
src/stage1hr-single.c

2023-09-06 15:16:47 -0700 Re-ordered methods for speed
src/method.c
src/method.h

2023-09-06 15:15:19 -0700 Uncommented code for Kmer_search_approx
src/kmer-search.c
src/kmer-search.h

2023-09-06 08:13:11 -0700 Not calling KMER_EXACT2 if transcriptome_align_p is true
src/stage1hr-single.c

2023-09-06 08:12:34 -0700 Removed extraneous call to printing left chop symbols
src/path-print-alignment.c

2023-09-06 07:33:37 -0700 Checking for TR_EXACT and TR_APPROX when deciding whether to call Transcript_remap
src/path-solve.c

2023-09-06 07:32:51 -0700 Using new interfaces to Stage1hr_single_setup and Stage1hr_paired_setup
src/gsnap.c

2023-09-06 07:32:26 -0700 Added debugging statements
src/intersect-simd.c

2023-09-06 07:32:11 -0700 Removed exact results from Intersect_approx
src/intersect.c
src/intersect.h

2023-09-06 07:31:49 -0700 Separated method TR_ENDS into TR_EXACT and TR_APPROX
src/method.c
src/method.h

2023-09-06 07:31:03 -0700 Using separated procedures for Transcriptome_search_exact and Transcriptome_search_approx
src/stage1hr-paired.c
src/stage1hr-paired.h

2023-09-06 07:30:33 -0700 Using separated procedures for Transcriptome_search_exact and Transcriptome_search_approx
src/stage1hr-single.c

2023-09-06 07:29:43 -0700 Implemented Stage1_init_oligos_tr and Stage1_init_positions_tr
src/stage1hr.c
src/stage1hr.h

2023-09-06 07:28:37 -0700 Implemented and tested binary search.  Computing exonend as needed, rather than computing all exonends
src/transcript-remap.c

2023-09-06 07:27:31 -0700 Fixed tests in TEST_BINARY_SEARCH
src/trpath.c

2023-09-06 07:26:44 -0700 Separated Transcriptome_search_ends into Transcriptome_search_exact and Transcriptome_search_approx
src/transcriptome-search.c
src/transcriptome-search.h

2023-09-06 07:25:50 -0700 Removed extraneous tab
src/path-print-alignment.c

2023-09-05 16:53:05 -0700 Changed field names in Transcript_T and Repair_T objects from tstart and tend to trstart and trend
src/repair.c
src/repair.h
src/transcript-remap.c
src/transcript.c
src/transcript.h

2023-09-05 16:37:08 -0700 Fixed _free_list and _gc procedures to set the list to be NULL
src/hitlistpool.c
src/hitlistpool.h
src/intlistpool.c
src/intlistpool.h
src/listpool.c
src/listpool.h
src/pathpool.h
src/transcriptpool.c
src/transcriptpool.h
src/trdiagpool.c
src/trdiagpool.h
src/uint8listpool.c
src/uint8listpool.h
src/uintlistpool.c
src/uintlistpool.h
src/univdiagpool.c
src/univdiagpool.h

2023-09-05 16:36:02 -0700 Computing transcript and exons in conversion procedures
src/trpath.c
src/trpath.h

2023-09-05 16:35:32 -0700 Using new interface to conversion procedures, and allowing those procedures to add a transcript to the path.  Fixed memory leak for Trpath_T objects.  Fixed memory leak for junctions resultin from List_head_set
src/trpath-solve.c

2023-09-05 16:34:13 -0700 Revised comments
src/transcriptome-search.c

2023-09-05 16:34:02 -0700 Fixed free_non_intersection to return remaining paths, and using the result to revise the transcript lists in Transcript_intersection
src/transcript.c

2023-09-05 16:32:11 -0700 Removed code for Transcript_remap_tr.  Computing of exons now performed by conversion procedures
src/transcript-remap.c

2023-09-05 16:30:46 -0700 Using new names for genomic fill_all_oligos and fill_all_positions procedures
src/stage1hr-paired.c

2023-09-05 16:30:20 -0700 Added debugging statements to Stage1_dump
src/stage1hr.c
src/stage1hr.h

2023-09-05 16:28:28 -0700 Removing transcripts where repair is unsuccessful
src/repair.c

2023-09-05 16:27:39 -0700 Fixed computation of remainder.  Added assertions
src/path-trim.c

2023-09-05 16:27:15 -0700 Revised try_repairs to return whether a repair was successful.  Fixed issue with pushing duplicate paths.  Fixed memory leak of junctions from List_head_set
src/path-solve.c

2023-09-05 16:25:45 -0700 Using new interface to Stage1hr_single_setup
src/gsnap.c

2023-09-05 16:25:17 -0700 Renamed Path_create_simple to Path_create_from_transcript, which now takes a transcript as a paramter
src/path.h

2023-09-05 16:24:44 -0700 Revised Path_common_structure_p to require the same trims from both paths.  Renamed Path_create_simple to Path_create_from_transcript, which now takes a transcript as a parameter
src/path.c

2023-09-05 16:23:25 -0700 Revised Path_consolidate to handle different patterns of trimming, and to defer paths that do not have a common structure with bestpath
src/path-eval.c
src/path-eval.h

2023-09-05 16:11:50 -0700 Separated computation of univdiagonals and paths.  Commented out kmer-approx method
src/kmer-search.c
src/kmer-search.h

2023-09-05 16:10:47 -0700 Rearranged order of methods.  Commented out kmer-approx method
src/method.c
src/method.h

2023-09-05 16:10:25 -0700 Rearranged order of methods to put transcriptome methods near the beginning.  For kmer-exact method, separated computation of univdiagonals and paths, and deferring computation of paths if there are too many univdiagonals.  Removing kmer-approx method, which can be very slow in some cases
src/stage1hr-single.c
src/stage1hr-single.h

2023-09-05 16:08:27 -0700 Crteated separate procedures for extend_seeds_union, extend_seeds_queryfwd, and extend_seeds_queryrev
src/tr-extension-search.c

2023-09-05 16:07:41 -0700 Created separate procedures for extend_seeds_union, extend_seeds_queryfwd, and extend_seeds_queryrev
src/extension-search.c

2023-09-05 06:10:43 -0700 Fixed compute_exons_simple
src/transcript-remap.c

2023-09-04 06:32:51 -0700 Implemented Transcript_list_trim
src/transcript.c
src/transcript.h

2023-09-04 06:25:57 -0700 Made fixes to binary search and linear search to advance to next exon when trstart == exonbounds[exoni]
src/trpath.c

2023-09-03 20:29:59 -0700 Calling Transcript_list_trim
src/path-eval.c

2023-09-03 20:29:10 -0700 Using new interfaces to Transcriptome_search_setup and Stage1hr_setup
src/gsnap.c

2023-09-03 20:28:44 -0700 Using fields and parameters for transcriptome computation
src/transcriptome-search.c
src/transcriptome-search.h

2023-09-03 20:28:10 -0700 Using Transcript_remap_tr instead of Transcript_remap
src/trpath-solve.c

2023-09-03 20:27:32 -0700 Streamlined conversion procedures, and using binary search.  Conversion procedures now returning overall_trstart and overall_trend.
src/trpath.c
src/trpath.h

2023-09-03 20:25:00 -0700 Separated fields and procedures for transcriptome and genome computations
src/stage1hr.c
src/stage1hr.h

2023-09-03 10:10:16 -0700 Implemented Path_common_structure_p
src/path.c
src/path.h

2023-09-03 10:09:22 -0700 Using new procedure names Path_trim_qstart_chrbounds and Path_trim_qend_chrbounds
src/pathpair-eval.c

2023-09-03 10:08:57 -0700 Implemented Path_trim_qstart_n and Path_trim_qend_n
src/path-trim.c
src/path-trim.h

2023-09-03 10:08:30 -0700 Implemented Path_consolidate
src/path-eval.c
src/path-eval.h

2023-09-01 16:36:29 -0700 Fixed printing of deletion strings
src/path-print-alignment.c

2023-09-01 16:34:53 -0700 In try_repairs_exact, making separate calls to Transcript_remap for sense_path and antisense_path
src/path-solve.c

2023-09-01 16:33:09 -0700 Using new interface to Transcript_remap
src/path-fusion.c

2023-09-01 16:32:39 -0700 Using new interface to Transcript_remap
src/trpath-solve.c

2023-09-01 16:31:57 -0700 Removed effective_sensedir as a parameter to Transcript_remap
src/transcript-remap.c
src/transcript-remap.h

2023-08-31 09:16:39 -0700 Using new interface to Path_print_alignment_setup
src/gsnap.c

2023-08-31 09:16:15 -0700 For intersections between valid and invalid ends, returning false for transcript_concordant_p
src/transcript.c

2023-08-31 09:15:42 -0700 Now following transcript_genestrand to avoid repairing by transcripts with the wrong sensedir
src/transcript-remap.c

2023-08-31 09:14:51 -0700 Calling Path_unique instead of Path_filter
src/stage1hr-single.c

2023-08-31 09:14:02 -0700 Shifting qdistal away from from 0 and querylength to avoid calling splices at the ends of the read
src/spliceends.c

2023-08-31 09:13:29 -0700 Added a debugging statement
src/repair.c

2023-08-31 09:13:16 -0700 No longer calling Transcript_intersection, now called by Pathpair_new_concordant
src/pathpair-eval.c

2023-08-31 09:12:42 -0700 Pathpair_new_concordant calling Transcript_intersection
src/pathpair.c

2023-08-31 09:11:59 -0700 Implemented Path_unique
src/path.c
src/path.h

2023-08-31 09:11:41 -0700 In Path_solve_from_ends, requiring that donor_prob and acceptor_prob be greater than 0.9.  In compute_qstart_local and compute_qend_local, saving splice_path and end_path, if both available.
src/path-solve.c

2023-08-31 09:09:05 -0700 Using method_print_p
src/path-print-alignment.c
src/path-print-alignment.h

2023-08-31 09:05:45 -0700 No longer checking nmismatches_allowed
src/path-fusion.c

2023-08-27 20:15:06 -0700 Removed queryseq5 and queryseq3 as parameters to Transcript_intersection
src/transcript.c
src/transcript.h

2023-08-27 20:13:05 -0700 When extending to the end of the read, setting splice5p, splicetype5, ambig_prob_5, splice3p, splicetype3, ambig_prob_3
src/repair.c

2023-08-27 20:12:05 -0700 Added a debugging statement
src/localdb-read.c

2023-08-26 10:46:55 -0700 Using new interface to Pathpair_setup
src/gsnap.c

2023-08-26 10:45:13 -0700 Checking whether there is room at the beginning or end of the genome to perform a resolve
src/pathpair.c
src/pathpair.h

2023-08-25 07:24:19 -0700 Using transcript_concordant_p in local_cmp and global_cmp.  Using insertlength and outerlength in local_cmp
src/pathpair-eval.c

2023-08-25 07:23:35 -0700 Added field transcript_concordant_p
src/pathpair.c
src/pathpair.h

2023-08-25 07:22:59 -0700 Transcript_intersection now returning whether valid concordant transcripts are found
src/transcript.c
src/transcript.h

2023-08-25 07:22:15 -0700 Path_qstart_resolve and Path_qend_resolve using the result of local_nmismatches from Spliceends_qstart_resolve and Spliceends_qend_resolve
src/path-fusion.c
src/path-solve.c

2023-08-25 07:20:37 -0700 Spliceends_qstart_resolve and Spliceends_qend_resolve now returning local_nmismatches
src/spliceends.c
src/spliceends.h

2023-08-25 07:20:01 -0700 Implemented Intlist_head_incr.  Made Intlist_head_set and Intlist_head_incr inline
src/intlist.c
src/intlist.h

2023-08-24 11:12:33 -0700 Changed Transcript_intersection procedure to simplify outputs when an intersection is present, and to allow discordant outputs when an intersection is not present
src/transcript.c

2023-08-24 11:09:14 -0700 Fixed reported intron lengths in debugging statements
src/transcript-remap.c

2023-08-24 11:08:18 -0700 In Path_qstart_resolve and Path_qend_resolve, considering a deletion in addition to a splice.  No longer checking nmismatches_allowed when combining left/right paths
src/path-solve.c

2023-08-24 11:07:01 -0700 Setting unextended fields of unextended paths after performing List_append to consolidate them
src/stage1hr-single.c

2023-08-24 11:03:45 -0700 In embellish genomic, changed assertion to allow for an empty segment, which can occur when a deletion occurs next to a splice junction
src/path-print-alignment.c

2023-08-24 11:02:51 -0700 Allowing deletions next to splices, which result in duplicated endpoints
src/path.c

2023-08-24 11:02:21 -0700 Rewrote Trpath_convert_to_path procedures
src/trpath.c

2023-08-24 11:01:34 -0700 For supplemental line, using path->fusion_chrnum instead of path->chrnum in deciding whether to output =
src/path-print-sam.c

2023-08-24 11:00:37 -0700 In Knownsplicing_from_transcriptome, converting 1-based coordinates from transcript map to 0-based coordinates
src/knownsplicing.c

2023-08-20 09:01:50 -0700 Preventing indel solutions beyond the end of the chromosome
src/indel.c
src/indel.h
src/path-solve.c
src/path.h
src/splice.c
src/splice.h
src/trpath-solve.c

2023-07-23 04:45:33 -0700 Updated for latest version
VERSION
config.site.rosalind.prd
config.site.rosalind.tst

2023-07-23 04:44:41 -0700 Updated for latest version
share/index.html

2023-07-21 00:51:53 -0700 Keeping only the best alignment in each overlapping group
src/path-eval.c

2023-07-21 00:51:40 -0700 Keeping only the best alignment in each overlapping group
src/pathpair-eval.c

2023-07-21 00:07:38 -0700 Using new interface to Knownsplicing_new
src/gsnap.c

2023-07-21 00:07:19 -0700 Knownsplicing_new takes intron_level_p as a parameter, needed for error checking
src/knownsplicing.c
src/knownsplicing.h

2023-07-21 00:01:39 -0700 Restored call to Sarray_long_on_short
src/gexact.c

2023-07-21 00:01:12 -0700 Fixed debugging statement
src/ef64.c

2023-07-21 00:01:03 -0700 Added debugging statements
src/spliceends.c

2023-07-21 00:00:10 -0700 Commented out code for Sarray_long_on_short_var_matches
src/sarray-read.c
src/sarray-read.h

2023-07-20 23:59:44 -0700 In Path_solve_from_diagonals, checking if qstart_univdiags and qend_univdiags are in the same chromosome as middle_univdiagonal
src/path-solve.c

2023-07-17 18:55:07 -0700 Using new interface to trpath-solve procedures
src/tr-extension-search.c
src/tr-extension-search.h

2023-07-17 18:54:39 -0700 Handling choplength and 3' UTRs
src/transcript-remap.c
src/transcript-remap.h

2023-07-17 18:53:45 -0700 Providing queryseq to Transcript_remap procedures
src/trpath-solve.c
src/trpath-solve.h

2023-07-17 18:53:14 -0700 Using new interface to trpath-solve procedures
src/transcriptome-search.c
src/transcriptome-search.h

2023-07-17 18:52:54 -0700 Added trlength as a field
src/transcript.c
src/transcript.h

2023-07-17 18:51:57 -0700 Stage1_list_paths now checks that the sensedir of each path is correct
src/stage1hr.c

2023-07-17 18:51:24 -0700 Using result of any_insufficient_p from kmer-search procedures.  Using new interfaces to path-fusion procedures
src/stage1hr-single.c
src/stage1hr-single.h

2023-07-17 18:50:37 -0700 Providing queryseq to path-solve procedures
src/stage1hr-paired.c

2023-07-17 18:49:47 -0700 Taking parameters to determine whether to chop poly-A on first end, second end, or both of a paired-end read
src/shortread.c
src/shortread.h

2023-07-17 18:48:59 -0700 Providing queryseq to Path_solve_from_diagonals
src/segment-search.c
src/segment-search.h

2023-07-17 18:48:16 -0700 Implemented Sarray_long_on_short_var_matches, which returns results on all suffixes
src/sarray-read.c
src/sarray-read.h

2023-07-17 18:47:42 -0700 Standardizing the order of parameters
src/path-fusion.c
src/path-fusion.h

2023-07-17 18:46:45 -0700 Fixed the printing of hardclips in supplemental cigars
src/path-print-sam.c

2023-07-17 18:46:21 -0700 Fixed a bug where unextended sense paths were being put into unextended_antisense_paths.  Using new interface to Transcript_remap
src/path-solve.c
src/path-solve.h

2023-07-17 18:45:02 -0700 Implemented Path_structure_cmp
src/path.c
src/path.h

2023-07-17 18:44:37 -0700 Implemented Pathpair_structure_cmp
src/pathpair.c
src/pathpair.h

2023-07-17 18:44:18 -0700 Removing duplicates at the beginning of Pathpair_eval_and_sort.  Handling different sensedirs separately in Pathpair_local_cmp.  Not optimizing on nmatches until after we find fusions
src/pathpair-eval.c

2023-07-17 18:42:02 -0700 Removing duplicates at the beginning of Path_eval_and_sort
src/path-eval.c
src/path-eval.h

2023-07-17 18:41:16 -0700 Returning the value of any_insufficient_p, so all kmers are treated the same
src/kmer-search.c
src/kmer-search.h

2023-07-17 18:39:55 -0700 Handling single-cell reads where poly-A is not expected in the first read
src/gsnap.c

2023-07-17 18:39:16 -0700 Using new interface to Shortread_setup
src/gfilter.c

2023-07-17 18:39:01 -0700 When the target is subsumed, counting nmatches as the length of the target, not the maximum substring matched
src/gexact.c

2023-07-17 18:38:11 -0700 Handling the case where queryfwd_best_elts is NULL or queryrev_best_elts is NULL
src/extension-search.c
src/extension-search.h

2023-07-17 18:35:06 -0700 Using new interface to Path_extend
src/concordance.c

2023-06-13 18:19:58 -0700 Using new interface to single_read_extend
src/stage1hr-paired.c

2023-06-13 18:19:46 -0700 Removed single-end fusion procedure from single_read_extend and created single_read_fusion
src/stage1hr-single.c
src/stage1hr-single.h

2023-06-13 17:49:40 -0700 Providing extend_qstart_p and extend_qend_p as parameters to Transcript_remap.  Computing tstart and tend without overhangs, and passing overhangs to Transcript_new
src/transcript-remap.c
src/transcript-remap.h

2023-06-13 17:44:10 -0700 Using new interface to Transcript_remap
src/trpath-solve.c

2023-06-13 17:43:57 -0700 Added tstart_overhang and tend_overhang fields.  Implement Transcript_fragment_length
src/transcript.c
src/transcript.h

2023-06-13 17:43:08 -0700 Calling Transcript_fragment_length instead of Transcript_intersection
src/stage1hr-paired.c

2023-06-13 17:42:53 -0700 Samread_get_aux_string now terminating at \0 character
src/samread.c

2023-06-13 17:42:26 -0700 Changed comment
src/repair.c

2023-06-13 17:42:15 -0700 Calling Transcript_intersection
src/pathpair-eval.c

2023-06-13 17:41:57 -0700 Using new interface to Transcript_remap
src/path-solve.c

2023-06-13 17:41:43 -0700 Using new interface to Transcript_remap
src/path-fusion.c

2023-06-13 17:40:58 -0700 Printing transcripts
src/compare2truth.c

2023-06-13 17:40:40 -0700 Added samread to compare2truth
src/Makefile.dna.am

2023-06-13 11:40:18 -0700 Merge branch 'master' of ssh.code.roche.com:/twu/gmap
2023-06-13 11:39:36 -0700 Fixed faulty merge into master.  Incorporated latest versions
src/access.c
src/compare2truth.c
src/equiv-class.c
src/equiv-class.h
src/extension-search.c
src/extension-search.h
src/gcount.c
src/genome.c
src/genomebits.c
src/gexact.c
src/gfilter.c
src/gmap.c
src/gsnap.c
src/inbuffer.c
src/inbuffer.h
src/indexdb.c
src/kmer-search.c
src/localdb-read.c
src/mem.c
src/method.h
src/path-eval.c
src/path-fusion.c
src/path-fusion.h
src/path-print-sam.c
src/path-solve.c
src/path-trim.c
src/path.c
src/pathpair-eval.c
src/pathpair-eval.h
src/record.h
src/repair.c
src/samread.c
src/samread.h
src/sarray-read.c
src/segment-search.c
src/segment-search.h
src/shortread.c
src/shortread.h
src/spliceends.c
src/stage1hr-paired.c
src/stage1hr-single.c
src/stage1hr-single.h
src/stage1hr.c
src/stage1hr.h
src/tr-extension-search.c
src/tr-extension-search.h
src/transcript-remap.c
src/transcript-velocity.c
src/transcript.c
src/transcriptome-search.c
src/transcriptome-search.h
src/transcriptome.c

2023-06-13 19:35:18 +0200 Merge branch 'stage1hr-def' into 'master'
2023-06-13 10:17:15 -0700 Hiding debugging procedures
src/stage1hr.c

2023-06-13 10:16:55 -0700 Turning off debugging macro
src/path.c

2023-06-13 09:44:47 -0700 Updated version number
VERSION
config.site.rosalind.prd
config.site.rosalind.tst

2023-06-13 09:43:21 -0700 Using new interface to Shortread_read
src/inbuffer.c
src/inbuffer.h

2023-06-13 09:42:47 -0700 Using new interface to Path_fusion_setup and Inbuffer_setup
src/gsnap.c

2023-06-13 09:42:16 -0700 Using new interface to Inbuffer_setup
src/gmap.c

2023-06-13 09:42:05 -0700 Using new interface to Inbuffer_setup
src/gfilter.c

2023-06-13 09:41:56 -0700 Changed warning message
src/compare2truth.c

2023-06-13 09:40:14 -0700 Using new interface to Inbuffer_setup
src/gexact.c

2023-06-13 09:29:26 -0700 Defining Storage_T as a Table_T object
src/gcount.c

2023-06-13 09:28:51 -0700 Calling single_read_extend.  No longer requiring transcripts to match for concordance
src/stage1hr-paired.c

2023-06-13 09:26:46 -0700 Implemented single_read_extend
src/stage1hr-single.c
src/stage1hr-single.h

2023-06-13 09:25:47 -0700 Added fields for extended paths
src/stage1hr.c
src/stage1hr.h

2023-06-13 09:25:27 -0700 Fixed criteria for paired-end retained intron
src/transcript-velocity.c

2023-06-13 09:24:31 -0700 Checking for duplicate fields in SAM file
src/samread.c

2023-06-13 09:24:11 -0700 Implemented Shortread_print_hardclipped_quality and Shortread_print_hardclipped_reverse_quality
src/shortread.c
src/shortread.h

2023-06-13 09:23:39 -0700 Calling new procedures for printing quality
src/path-print-sam.c

2023-06-13 09:23:17 -0700 Added debugging statements
src/path.c

2023-06-13 09:23:07 -0700 Added debugging statemenst
src/repair.c

2023-06-13 09:22:37 -0700 Using new Id tag
src/mem.h

2023-06-13 09:22:25 -0700 Formatting change
src/mem.c

2023-06-08 11:14:06 -0700 Using arrays instead of lists to store trnums and weights
src/equiv-class.c
src/equiv-class.h

2023-06-08 11:13:30 -0700 Formatting change
src/Makefile.dna.am

2023-06-08 09:23:32 -0700 Assigning velocity to fusion transcripts
src/transcript-velocity.c

2023-06-08 09:23:14 -0700 No longer extending transcript coords to the end of the alignment, which is not valid for fusion alignments
src/transcript-remap.c

2023-06-08 09:22:44 -0700 Using new interface to Path_fusion procedures
src/stage1hr-paired.c
src/stage1hr-single.c

2023-06-08 09:22:16 -0700 Not chopping for poly-AT if the read contains the barcodes for single-cell reads
src/shortread.c
src/shortread.h

2023-06-08 09:21:25 -0700 Using new interface to Path_fusion procedures
src/pathpair-eval.c
src/pathpair-eval.h

2023-06-08 09:21:08 -0700 Removed unused variables
src/path-solve.c

2023-06-08 09:20:57 -0700 Moved single-cell fields to the end of the output
src/path-print-sam.c

2023-06-08 09:20:32 -0700 Computing transcripts after creating a fusion alignment
src/path-fusion.c
src/path-fusion.h

2023-06-07 14:06:21 -0700 Moved TR_COMPLETE after SEG1
src/method.h

2023-06-07 14:06:03 -0700 Looking only at last 3 positions on 3' end
src/transcriptome-search.c

2023-06-07 14:04:52 -0700 Initializing velocity field.  Copying velocity field
src/transcript.c

2023-06-07 14:04:33 -0700 Changed an assertion about trdiagonal
src/tr-extension-search.c

2023-06-07 14:03:58 -0700 Added an assertion about querylength
src/stage1hr.c

2023-06-07 14:03:38 -0700 Moved TR_COMPLETE method after SEG1
src/stage1hr-single.c

2023-06-07 14:03:03 -0700 Computing diagterm from queryoffset
src/segment-search.c

2023-06-07 14:01:48 -0700 Procedure for getting single-cell info no longer parses for transcripts
src/samread.c
src/samread.h

2023-06-07 14:00:57 -0700 Rearranged lines
src/path-print-sam.c

2023-06-07 14:00:44 -0700 Implemented a procedure try_repairs, and applying it to unextended paths.  Allowing splicing within circular chromosomes
src/path-solve.c

2023-06-07 13:59:56 -0700 Checking before subtracting linear_chrlength from univdiagonal.  Handles the cases where a splice occurs at the circular origin.
src/path-trim.c

2023-06-07 13:59:15 -0700 Path_print now prints information about circular alignment
src/path.c

2023-06-07 13:58:42 -0700 Handling reads shorter than min_querylength.  Changed default memory for localdb to be mmap
src/gsnap.c

2023-06-07 13:39:06 -0700 Computing pos5 and pos3 as parameters for mismatches, based on spliceend possibilities.  Allowing for circular splicing.
src/spliceends.c

2023-06-07 13:38:13 -0700 Disallowing translocations involving circular chromosomes, but allowing splicing within the same circular chromosome
src/path-fusion.c
src/path-fusion.h

2023-06-07 13:37:38 -0700 Added debugging statements
src/path-eval.c

2023-06-07 13:36:48 -0700 Created Storage_T object to hold lists of equiv classes.  Using a table to associate a Storage_T object with each cell name
src/gcount.c

2023-06-07 13:36:03 -0700 Restructured data so each cell_name has lists of equivalence classes
src/equiv-class.c
src/equiv-class.h

2023-06-07 13:34:21 -0700 Using FREE_KEEP for memory allocated privately
src/genome.c
src/genomebits.c
src/indexdb.c
src/localdb-read.c
src/sarray-read.c
src/transcriptome.c

2023-06-07 13:32:52 -0700 Changed Access_allocate_private to use the keep category of memory
src/access.c

2023-06-05 10:55:15 -0700 Added features for single-cell alignments
src/equiv-class.c
src/equiv-class.h
src/gcount.c

2023-05-29 21:44:35 -0700 Using new interfaces to setup procedures.  Renamed indexdb2 to be indexdb_nonstd
src/gsnap.c

2023-05-29 21:43:53 -0700 No longer calling Stage1_integrate_end_positions.  Using new procedure Stage1_fill_all_positions
src/stage1hr-paired.c
src/stage1hr-single.c

2023-05-29 21:42:55 -0700 Following code for extension-search, using new format for Stage1_T objects
src/tr-extension-search.c
src/tr-extension-search.h

2023-05-29 21:42:02 -0700 Computing minus diagterms correctly
src/transcriptome-search.c
src/transcriptome-search.h

2023-05-29 21:40:27 -0700 Providing plusp to procedures.  Iterating over queryoffset and converting to querypos
src/record.h
src/segment-search.c
src/segment-search.h

2023-05-29 20:55:28 -0700 Using new locations of minus positions in Stage1_T object.  Converting from queryoffset to querypos and querypos_rc
src/extension-search.c
src/extension-search.h

2023-05-29 20:53:42 -0700 Using renamed fields end5 and end3 in Stage1_T object
src/kmer-search.c

2023-05-29 20:52:51 -0700 Assigning values to positions during Stage1_init, rather than in a subsequent call to Stage1_integrate_end_positions.  Storing positions in the same querypos and forward_oligos and revcomp_oligos
src/stage1hr.c

2023-05-29 20:50:48 -0700 Keeping a single array for validp
src/stage1hr.h

2023-05-29 15:06:06 -0700 Updated version number
VERSION
config.site.rosalind.prd
config.site.rosalind.tst

2023-05-29 15:00:12 -0700 Using new interface to Indel_resolve procedures
src/trpath-solve.c

2023-05-29 14:59:34 -0700 Setting nexons field in Transcript_copy
src/transcript.c

2023-05-29 14:59:20 -0700 Added an assertion
src/transcript-velocity.c

2023-05-29 14:59:10 -0700 Counting extensions past UTR bounds as utrp, and excluding them from consideration
src/transcript-remap.c

2023-05-29 14:58:21 -0700 Modified debugging statements
src/spliceends.c

2023-05-29 14:58:09 -0700 Using new interface to Indel_resolve procedures
src/splice.c

2023-05-29 14:57:19 -0700 Using new interface to Indel_resolve procedures
src/path-solve.c

2023-05-29 14:56:57 -0700 Removed check on mismatches_allowed
src/indel.c
src/indel.h

2023-05-29 14:56:33 -0700 Computing weights as 1.0/npossibilities, for each fragment length
src/gcount.c

2023-05-29 14:54:35 -0700 Computing weights as 1.0/npossibilities, determined by each fragment length
src/equiv-class.c
src/equiv-class.h

2023-05-29 14:52:53 -0700 Added comment
src/compare2truth.c

2023-05-28 15:20:03 -0700 Implemented Exon_list_consecutivep
src/exon.c
src/exon.h

2023-05-28 15:19:39 -0700 Repair_path no longer freeing repair
src/repair.c

2023-05-28 15:19:06 -0700 Using new interface to Transcript_remap
src/path-solve.c
src/trpath-solve.c

2023-05-28 15:18:48 -0700 Disallowing alignments to UTRs and non-consecutive exons.  Transcript_remap returning single lists of transcripts, invalid transcripts, and repairs
src/transcript-remap.c
src/transcript-remap.h

2023-05-28 15:17:29 -0700 Treating one-exon genes as spliced
src/transcript-velocity.c

2023-05-28 15:16:59 -0700 Added field nexons
src/transcript.c
src/transcript.h

2023-05-28 13:34:51 -0700 Initial implementation of gcount
src/Makefile.dna.am
src/equiv-class.c
src/equiv-class.h
src/gcount.c

2023-05-27 15:59:14 -0700 Calling Transcript_velocity procedures
src/stage1hr-paired.c
src/stage1hr-single.c

2023-05-27 15:58:52 -0700 Always returning a value from Stage1_new, even if querylength < index1part
src/stage1hr.c

2023-05-27 15:58:20 -0700 Printing velocities
src/transcript.c
src/transcript.h

2023-05-27 15:57:57 -0700 Added computation of velocities
src/Makefile.dna.am
src/Makefile.gsnaptoo.am
src/transcript-velocity.c
src/transcript-velocity.h

2023-05-27 15:57:26 -0700 Restored extension of coords to ends of the query sequence, needed for correct computation of overhang for repairs
src/transcript-remap.c

2023-05-27 12:34:29 -0700 Checking that result of inner fusion procedures is not NULL
src/stage1hr-paired.c

2023-05-27 12:34:03 -0700 Repair_path now removing invalid transcripts from path
src/repair.c
src/repair.h

2023-05-27 12:33:36 -0700 Added checks for transcripts being in ascending order.  Modified procedures to make use of sorted transcripts
src/transcript.c
src/transcript.h

2023-05-27 12:32:57 -0700 Excluding the case where an intron alignment is combined with other regions.  Sorting transcripts explicitly
src/transcript-remap.c

2023-05-27 12:31:59 -0700 Tableuint_keys_by_timeindex now handling the case where the table has length 0
src/tableuint.c

2023-05-27 06:01:29 -0700 Renamed variables.  Making use of Transcriptome_trnum function
src/gcount-bulk.c

2023-05-26 16:06:00 -0700 Handling cases where entire queryseq has been chopped.  Providing repetitive_ef64 to search procedures
src/gsnap.c

2023-05-26 16:05:13 -0700 Using new interface to Oligo_setup
src/gmap.c

2023-05-26 16:04:58 -0700 Allowing invalid transcripts to be sufficient
src/transcript-remap.c

2023-05-26 16:04:44 -0700 Using new interface to Reader_new procedure
src/transcriptome-search.c

2023-05-26 16:04:32 -0700 Accounting for chop lengths in computing fragment length
src/transcript.c
src/transcript.h

2023-05-26 16:04:06 -0700 Using new interface to Reader_new procedure
src/stage1hr.c

2023-05-26 16:03:49 -0700 Using new interface to segment search procedures
src/stage1hr-single.c
src/stage1hr-single.h

2023-05-26 16:03:23 -0700 Using new interfaces to concordance procedures and segment search procedures
src/stage1hr-paired.c
src/stage1hr-paired.h

2023-05-26 16:02:45 -0700 Using new interface to Reader_new
src/stage1.c

2023-05-26 16:02:29 -0700 Ensuring that all splice sites are included in call to Genome_mismatches for known splicing
src/spliceends.c

2023-05-26 16:01:53 -0700 Removed unused procedure
src/kmer-search.c

2023-05-26 16:01:27 -0700 Using new interface to Reader_new and Oligo_setup
src/gfilter.c

2023-05-26 16:01:06 -0700 Removed debugging macro around a printing procedure
src/exon.c

2023-05-26 16:00:47 -0700 Using new interface to Pathpair_new_concordant
src/concordance.c
src/concordance.h

2023-05-26 16:00:31 -0700 Using new interface to Path_print procedures
src/output.c

2023-05-26 16:00:17 -0700 Handling chopped ends
src/path-print-alignment.c
src/path-print-alignment.h

2023-05-26 16:00:01 -0700 No longer printing XP field for primer sequence.  Path_cigar_md now accounting for chopped ends
src/path-print-sam.c
src/path-print-sam.h

2023-05-26 15:59:15 -0700 Using oligosize from Reader_T
src/oligo.c
src/oligo.h

2023-05-26 15:58:55 -0700 Moved definition of Reader_T to be extern, and using inline procedures.  Added oligosize as a field in Reader_T
src/reader.c
src/reader.h

2023-05-26 15:58:17 -0700 Using new interface to Pathpair_new_concordant
src/pathpair-eval.c
src/pathpair-eval.h

2023-05-26 15:57:44 -0700 Using chop lengths in computing insertlength
src/pathpair.c
src/pathpair.h

2023-05-26 15:56:55 -0700 Implemented EF64_from_oligos and EF64_presentp
src/ef64.c
src/ef64.h

2023-05-26 15:56:33 -0700 Ignoring repetitive oligos instead of relying upon a limit to the number of positions
src/segment-search.c
src/segment-search.h

2023-05-26 15:56:02 -0700 Added repetitive.c
src/Makefile.dna.am
src/Makefile.gsnaptoo.am
src/repetitive.c
src/repetitive.h

2023-05-26 15:55:44 -0700 Incorporated code from chop.c into shortread.c.  Allowing fulllength to be 0 in reading shortreads
src/chop.c
src/chop.h
src/shortread.c

2023-05-26 09:33:30 -0700 Added a step to remove poly-A/T regions from the ends of reads
src/Makefile.dna.am
src/Makefile.gsnaptoo.am
src/chop.c
src/chop.h
src/shortread.c
src/shortread.h

2023-05-25 13:31:22 -0700 Formatting change
src/uint8listpool.h

2023-05-25 13:30:47 -0700 Added transcriptome.c to trindex
src/Makefile.dna.am
src/Makefile.gsnaptoo.am

2023-05-25 13:29:47 -0700 Implemented Pathpair_transcript_intersectp
src/pathpair.c
src/pathpair.h

2023-05-25 13:29:34 -0700 Calling Transcript_print_nums in Path_print
src/path.c

2023-05-25 13:29:09 -0700 Undefining debugging macro
src/path-solve.c

2023-05-25 13:28:54 -0700 Printing both XX and XY fields
src/path-print-sam.c

2023-05-25 13:28:38 -0700 Providing nalignments to Knownsplicing_from_transcriptome
src/gsnap.c

2023-05-25 13:28:16 -0700 In Knownsplicing_from_transcriptome, iterating of map_index and then calling Transcriptome_trnum
src/knownsplicing.c
src/knownsplicing.h

2023-05-25 13:27:21 -0700 Using new interface to Path_extend
src/concordance.c
src/concordance.h

2023-05-25 13:26:53 -0700 Added include of uintlistpool.h
src/extension-search.h

2023-05-25 13:26:36 -0700 Added include of uintlistpool.h
src/kmer-search.h

2023-05-25 13:26:14 -0700 Added include of uintlistpool.h
src/segment-search.h

2023-05-25 13:25:59 -0700 Using new interface to Path_extend and Concordance_simple
src/stage1hr-paired.c

2023-05-25 13:25:45 -0700 Using new interface to Path_extend
src/stage1hr-single.c

2023-05-25 13:25:11 -0700 Using new macro for Stage1_init debugging statements
src/stage1hr.c
src/stage1hr.h

2023-05-25 13:24:22 -0700 Added missing struct
src/uint8listpool.c

2023-05-25 13:22:31 -0700 Calling EF64_chrnum and Transcriptome_exons in that order
src/trpath-solve.c

2023-05-25 13:21:49 -0700 Computing and saving dbindex file.  Added check_data step
src/trindex.c

2023-05-25 12:59:44 -0700 Added field for dbindex
src/transcriptome.c
src/transcriptome.h

2023-05-25 12:58:16 -0700 Computing intersection between valid and invalid transcripts
src/transcript.c
src/transcript.h

2023-05-25 12:57:33 -0700 Distinguishing between map_index and trnum.  No longer extending exon coords to end of queryseq
src/transcript-remap.c

2023-05-25 12:56:07 -0700 Repair_path now running Path_eval_nmatches
src/repair.c
src/repair.h

2023-05-25 12:55:47 -0700 Using new interface to Repair_path.  Computing transcripts in Path_extend
src/path-solve.c
src/path-solve.h

2023-05-23 08:17:45 -0700 Using oligos in Stage1_T object
src/transcriptome-search.c
src/transcriptome-search.h

2023-05-23 08:16:14 -0700 Renamed categories for transcriptome-based search
src/method.c
src/method.h

2023-05-23 08:15:38 -0700 Added Tr_extension_search
src/stage1hr-paired.c
src/stage1hr-paired.h

2023-05-23 08:15:23 -0700 Added Tr_extension_search
src/stage1hr-single.c
src/stage1hr-single.h

2023-05-23 08:15:05 -0700 Created new debugging macro for nosplice trimming
src/spliceends.c

2023-05-23 07:58:46 -0700 Modified debugging statements
src/path-solve.c

2023-05-23 07:58:33 -0700 Using newly named fields in Stage1_T object for end positions
src/kmer-search.c

2023-05-23 07:57:32 -0700 Added trdiagpool
src/gsnap.c

2023-05-23 07:57:05 -0700 Adjusting endpoints in geneminus case for insertions
src/trpath.c
src/trpath.h

2023-05-23 07:56:31 -0700 Handling the case where the left or right trdiagonal is equal to the middle trdiagonal
src/trpath-solve.c

2023-05-23 07:55:41 -0700 Added file for tr-extension-search
src/tr-extension-search.h

2023-05-23 07:55:22 -0700 Modified debugging statements
src/tr-extension-search.c

2023-05-23 07:55:05 -0700 Added tr_queryfwd and tr_queryrev sets from tr-extension-search
src/stage1hr.c
src/stage1hr.h

2023-05-23 07:46:56 -0700 Modified debugging statement
src/extension-search.c

2023-05-23 07:46:37 -0700 Made EF64_trnum follow code in EF64_chrnum
src/ef64.c
src/ef64.h

2023-05-23 07:46:09 -0700 Added files for transcriptome extension search
src/Makefile.dna.am
src/Makefile.gsnaptoo.am
src/trdiag.c
src/trdiag.h
src/trdiagdef.h
src/trdiagpool.c
src/trdiagpool.h

2023-05-22 17:26:39 -0700 Trpath_solve_from_diagonals taking left and right trdiagonal, as well as bounds on the middle trdiagonal
src/trpath-solve.c
src/trpath-solve.h

2023-05-22 17:20:46 -0700 Initial import
src/tr-extension-search.c

2023-05-22 08:52:47 -0700 Using new procedure name Stage1_integrate_end_positions for Stage1_rearrange
src/stage1hr-paired.c
src/stage1hr-single.c

2023-05-22 08:52:06 -0700 Added positions arrays for transcriptome-based methods.  Renamed rawpositions arrays to positions_end
src/stage1hr.c
src/stage1hr.h

2023-05-21 06:19:52 -0700 Using new interface to Trpath_solve_from_diagonal
src/transcriptome-search.c

2023-05-21 06:19:23 -0700 Added qstart_trdiag and qend_trdiag as parameters
src/trpath-solve.c
src/trpath-solve.h

2023-05-21 06:17:52 -0700 Renamed Stage1_rearrange to Stage1_rearrange_genome
src/stage1hr.c
src/stage1hr.h

2023-05-21 06:16:53 -0700 Moved transcriptome search after kmer approx
src/stage1hr-single.c

2023-05-21 06:16:20 -0700 Modified debugging statement
src/path-solve.c

2023-05-21 06:16:00 -0700 Not printing invalid transcripts on multimappers
src/path-print-sam.c

2023-05-21 05:13:15 -0700 Using new interface to Extension_search_setup.  Setting transcriptome_align_p correctly when no transcriptome is given
src/gsnap.c

2023-05-21 05:12:31 -0700 Removed chromosome_iit from Extension_search_setup
src/extension-search.c
src/extension-search.h

2023-05-20 12:48:57 -0700 Calling Knownsplicing_from_transcriptome.  Relying upon search procedures to perform transcript remapping
src/gsnap.c

2023-05-20 12:48:08 -0700 Added a best_trimpos_adj variable which accounts for insertions
src/genomebits_indel.c

2023-05-20 12:47:31 -0700 Added a paired_read_transcriptome_search step.  Relying upon search procedures to perform transcript remapping
src/stage1hr-paired.c
src/stage1hr-paired.h

2023-05-20 12:46:29 -0700 Moved transcriptome search procedures after kmer approx step.  Relying upon search procedures to perform transcript remapping
src/stage1hr-single.c
src/stage1hr-single.h

2023-05-20 12:45:15 -0700 Added storage for Transcriptome_search procedures to Stage1_T object
src/stage1hr.h

2023-05-20 12:38:59 -0700 Setting values in medial_nmismatches for knownsplicing procedures
src/spliceends.c

2023-05-20 12:38:12 -0700 Implemented Knownsplicing_from_transcriptome
src/knownsplicing.c
src/knownsplicing.h

2023-05-20 12:37:36 -0700 Using new interface to Path_solve procedures
src/extension-search.c
src/extension-search.h
src/kmer-search.c
src/kmer-search.h
src/segment-search.c
src/segment-search.h

2023-05-20 12:37:01 -0700 Using new interface to Trpath_solve procedures
src/transcriptome-search.c
src/transcriptome-search.h

2023-05-20 12:36:14 -0700 Using new interface to Transcript_remap.  Returning found_transcriptp
src/path-solve.c
src/path-solve.h

2023-05-20 12:35:40 -0700 Using new interface to Transcript_remap
src/trpath-solve.c
src/trpath-solve.h

2023-05-20 12:35:06 -0700 Moved Transcript_intersection from transcript-remap.c  Implemented Transcript_intersectp
src/transcript.c
src/transcript.h

2023-05-20 12:34:31 -0700 Transcript_remap returning found_transcriptp.  Moved Transcript_intersection to transcript.c
src/transcript-remap.c
src/transcript-remap.h

2023-05-20 12:32:27 -0700 Added parameter to require transcript intersection
src/concordance.c
src/concordance.h

2023-05-16 18:51:57 -0700 Computing tstart and tend by extending to the beginning and end of queryseq
src/transcript-remap.c

2023-05-16 18:31:26 -0700 Computing splice distances correctly.  Extending coords to the beginning and end of queryseq
src/transcript-remap.c

2023-05-16 18:30:24 -0700 Checking whether the return value of Repair_path is NULL
src/path-solve.c

2023-05-16 18:29:46 -0700 Repair_path now checking for monotonicity of endpoints, setting nmismatches correctly, and removing alts.  Can return NULL
src/repair.c

2023-05-16 15:54:47 -0700 Using new interface to Path_solve_from_ends
src/kmer-search.c
src/kmer-search.h

2023-05-16 15:54:16 -0700 Using new interface to Path_solve_from_diagonals
src/extension-search.c
src/extension-search.h
src/segment-search.c
src/segment-search.h

2023-05-16 15:53:40 -0700 Calling Transcript_remap in all Trpath_solve procedures
src/trpath-solve.c
src/trpath-solve.h

2023-05-16 15:53:06 -0700 Renamed conversion procedures to have geneplus and geneminus
src/trpath.c
src/trpath.h

2023-05-16 15:52:40 -0700 Distinguishing variable names for gplusp and geneplusp
src/transcriptome-search.c
src/transcriptome-search.h

2023-05-16 15:52:07 -0700 Added desired_genestrand parameter to Transcript_remap.  Fixed computation of repair parameters
src/transcript-remap.c
src/transcript-remap.h

2023-05-16 15:51:13 -0700 Calling Transcriptome_remap and Repair_path in all Path_solve procedures
src/path-solve.c
src/path-solve.h

2023-05-16 15:50:35 -0700 Freeing repair
src/repair.c

2023-05-16 15:50:14 -0700 Fixed uninitialized variable in Exon_list_validp
src/exon.c

2023-05-16 12:06:47 -0700 Using new interfaces to Trpath_convert procedures
src/trpath-solve.c

2023-05-16 12:06:00 -0700 Fixed computation of plusp for path.  Fixed computation of trstart
src/trpath.c
src/trpath.h

2023-05-16 12:03:22 -0700 Fixed assignment of plusp to paths
src/transcriptome-search.c

2023-05-16 11:59:49 -0700 Using new inteface to Path_copy
src/path-fusion.c

2023-05-16 11:59:02 -0700 Using new interface to Pathpair_new_concordant
src/concordance.c

2023-05-16 11:58:45 -0700 Path_filter now considering splice prob in addition to nmatches.  Using new interface to Path_copy
src/pathpair.c
src/pathpair.h

2023-05-16 11:58:07 -0700 Pathpair_local_cmp and Pathpair_global_cmp now prioritizing based on presence of transcripts
src/pathpair-eval.c

2023-05-16 11:56:50 -0700 Path_local_cmp and Path_global_cmp now prioritizing based on presence of transcripts
src/path-eval.c

2023-05-16 11:55:22 -0700 Using new interface to Path_solve_exact
src/kmer-search.c
src/kmer-search.h

2023-05-16 11:55:02 -0700 Path_solve_exact now applying repairs from transcriptome
src/path-solve.c
src/path-solve.h

2023-05-16 11:54:29 -0700 Path_copy now copying transcripts
src/path.c
src/path.h

2023-05-16 11:52:58 -0700 Implemented Transcript_repair_tstart and Transcript_repair_tend
src/transcript.c
src/transcript.h

2023-05-16 11:52:40 -0700 Fixed some issues in computing exons.  Transcript_remap now returning repairs.  Transcript_remap_intersection returning fragment length based on transcripts
src/transcript-remap.c
src/transcript-remap.h

2023-05-16 11:33:52 -0700 Improved Exon_list_validp and returning repairablep
src/exon.c
src/exon.h

2023-05-16 11:33:00 -0700 Added repair.c and repair.h
src/Makefile.dna.am
src/Makefile.gsnaptoo.am
src/repair.c
src/repair.h

2023-05-12 05:42:34 -0700 Merged changes from master
2023-05-11 07:57:43 -0700 Added files and instructions for gcount-bulk and gcount-sc
src/Makefile.dna.am
src/equiv-class-bulk.c
src/equiv-class-bulk.h
src/equiv-class-sc.c
src/equiv-class-sc.h
src/gcount-bulk.c
src/gcount-sc.c
src/transcript-splice.c
src/transcript-splice.h

2023-05-11 07:56:45 -0700 Replaced old Id info with new Id tag
src/concordance.c
src/concordance.h
src/extension-search.c
src/extension-search.h
src/gsnap.c
src/hitlistpool.c
src/hitlistpool.h
src/intlistpool.c
src/intlistpool.h
src/junction.c
src/junction.h
src/kmer-search.c
src/kmer-search.h
src/list.h
src/listpool.c
src/listpool.h
src/mem.c
src/path-solve.c
src/path-solve.h
src/resulthr.c
src/resulthr.h
src/segment-search.c
src/segment-search.h
src/splice.c
src/stage1hr.c
src/stage1hr.h
src/transcript.c
src/transcript.h
src/uint8list.c
src/uint8list.h
src/uint8listpool.c
src/uint8listpool.h
src/uintlist.c
src/uintlist.h
src/uintlistpool.c
src/uintlistpool.h
src/univcoord.h
src/univdiagpool.c
src/univdiagpool.h

2023-05-11 07:52:40 -0700 Replacing old Id info with new Id tag
src/bitpack64-readtwo.c

2023-05-11 15:15:37 +0200 Merge branch 'reuse-memory-pools' into 'master'
2023-05-11 06:06:32 -0700 Removed reference to mpi directory
bootstrap.gsnaptoo

2023-05-11 06:06:17 -0700 Added call to automake
bootstrap.dna

2023-05-11 06:05:52 -0700 Updated for latest version
share/index.html

2023-05-01 13:26:24 -0700 Further checking whether localdb is present before calling Localdb_get
src/spliceends.c

2023-05-01 13:22:55 -0700 Not calling Localdb_get if therre is no localdb
src/spliceends.c

2023-05-01 12:21:01 -0700 Checking if nosplice trimpos would trim the alignment past the chromosomal start or end
src/path-solve.c

2023-05-01 12:20:00 -0700 No longer trimming if it would eliminate all segments
src/path-trim.c

2023-05-01 12:19:36 -0700 Added debugging statements
src/ef64.c

2023-05-01 12:19:23 -0700 Using new $Id$ tag
src/bitpack64-readtwo.c

2023-05-01 10:12:53 -0700 Updated for latest version
VERSION
config.site.rosalind.prd
config.site.rosalind.tst

2023-05-01 10:12:06 -0700 Turned off debugging macro
src/path.c

2023-05-01 10:11:54 -0700 Hiding Stage1_list_paths with macros
src/stage1hr.c

2023-04-29 11:23:05 -0700 Added a placeholder for PATHPOOL_REUSE
src/pathpool.h

2023-04-29 11:22:26 -0700 Using Id tag
src/uint8listpool.h

2023-04-29 11:22:14 -0700 Using Id tag
src/univdiagpool.h

2023-04-29 11:19:58 -0700 Changed an occurrence of INTLISTPOOL_REUSE to UINTLISTPOOL_REUSE
src/uintlistpool.h

2023-04-29 11:13:11 -0700 Using new interface to Path_extend
src/concordance.c

2023-04-29 11:12:44 -0700 In Stage1_free, free_paths_p now covers the unextended paths also
src/stage1hr.c

2023-04-29 11:11:35 -0700 Cleaned up the algorithm for extending paths and finding single-end fusions
src/stage1hr-single.c

2023-04-29 11:10:30 -0700 Using new interface to Path_extend
src/stage1hr-paired.c

2023-04-29 11:10:14 -0700 Turned off debugging macros
src/path-fusion.c

2023-04-29 11:09:58 -0700 Path_gc now setting the list to be NULL
src/path.c

2023-04-29 11:09:02 -0700 Path_extend now determining whether paths are complete at both ends and returning completep
src/path-solve.c
src/path-solve.h

2023-04-29 06:01:51 -0700 Initializing fusion_paths before each source of fusions.  Removed unused code using Path_extend
src/path-fusion.c

2023-04-28 15:12:13 -0700 Turned on inner fusions again
src/stage1hr-paired.c

2023-04-28 15:12:00 -0700 Handling issues involving the last position in the array returned by Genomebits_mismatches
src/splice.c

2023-04-28 15:11:13 -0700 Fixed values for inner fusions
src/path-fusion.c

2023-04-28 11:59:31 -0700 Fixed revisions of querystart5 and queryend3 for insertions
src/path-fusion.c

2023-04-27 21:57:40 -0700 Fixed issues with uninitialized variables
src/stage1hr-paired.c

2023-04-27 21:57:24 -0700 Increased value of SIGNIFICANT_COUNT.  Fixed uninitialized variable
src/segment-search.c

2023-04-27 21:57:02 -0700 Turned off debugging macro
src/path.c

2023-04-27 21:56:52 -0700 Removed debugging command
src/path-solve.c

2023-04-27 21:56:39 -0700 Turned off debugging macros
src/path-eval.c

2023-04-27 21:23:08 -0700 Implemented Univcoordlist_equal
src/uint8list.c
src/uint8list.h
src/uintlist.c
src/uintlist.h
src/univcoord.h

2023-04-27 21:22:57 -0700 Fixed a memory leak
src/stage1hr-single.c

2023-04-27 21:22:42 -0700 In paired_read_segment_search, handling the unextended and complete paths separately from the Stage1_T object, and integrating them later.  Performing a concordance step on the unextended paths
src/stage1hr-paired.c

2023-04-27 21:20:20 -0700 Added a debugging statement
src/pathpair-eval.c

2023-04-27 21:20:07 -0700 Fixed the recursive behavior of compute_qstart_local and compute_qend_local
src/path-solve.c

2023-04-27 21:18:57 -0700 Added a parameter SIGNIFICANT_COUNT and considering any univdiagonals that meet that count
src/segment-search.c

2023-04-27 21:18:15 -0700 Not using ambig probs to count as matches in Path_eval_nmatches.  Added a step in Path_eval_and_sort to remove main/fusion identical paths
src/path-eval.c

2023-04-27 21:17:13 -0700 Fixed code for outer fusions and single-end fusions to handle multiple exons in fusion and main paths
src/path-fusion.c

2023-04-27 19:48:51 -0700 In Stage1_list_paths, no longer tracing endpoints
src/stage1hr.c

2023-04-27 19:48:20 -0700 Removed a debugging abort
src/splice.c

2023-04-27 19:46:40 -0700 After Altsplice_free, ensuring that the value for qstart_alts or qend_alts is NULL
src/pathpair.c

2023-04-27 19:45:58 -0700 Made Path_extend_fwd and Path_extend_rev inline procedures and allowing for repeated endpoints
src/path.c
src/path.h

2023-04-27 19:45:15 -0700 Added a debugging statement
src/path-print-alignment.c

2023-04-27 19:39:47 -0700 Modified debugging procedures
src/path-eval.c

2023-04-27 19:39:15 -0700 Made List_pop_keep an inline procedure
src/list.c
src/list.h

2023-04-26 19:25:46 -0700 Including both algorithms for memory pools, one that re-uses cells and one that uses only new cells
src/hitlistpool.c
src/hitlistpool.h
src/intlistpool.c
src/intlistpool.h
src/listpool.c
src/listpool.h
src/pathpool.c
src/pathpool.h
src/transcriptpool.c
src/transcriptpool.h
src/trpathpool.c
src/trpathpool.h
src/uint8listpool.c
src/uint8listpool.h
src/uintlistpool.c
src/uintlistpool.h
src/univdiagpool.c
src/univdiagpool.h

2023-04-26 19:23:02 -0700 Checking over two regions to filter diagonals against low_univdiagonal and high_univdiagonal
src/localdb-read.c

2023-04-26 19:22:37 -0700 Modified comments
src/path-solve.c

2023-04-26 16:10:05 -0700 Formatting change
src/stage1hr.c

2023-04-26 16:09:14 -0700 Removed declaration of macro
src/path.c

2023-04-26 14:14:57 -0700 If singlepaths5 or singlepaths3 is NULL, then not generating patharray5 or patharray3
src/stage1hr-paired.c

2023-04-26 14:14:19 -0700 Modified debugging statement
src/resulthr.c

2023-04-26 14:14:10 -0700 If npaths is 0, then ensuring that *npaths_primary and *npaths_altloc are 0
src/pathpair-eval.c

2023-04-26 14:13:42 -0700 If npaths is 0, then ensuring that *npaths_primary and *npaths_altloc are 0
src/path-eval.c

2023-04-26 11:48:31 -0700 Leaving the initial chunk in place, instead of freeing it and adding it back again, between each query
src/gsnap.c
src/hitlistpool.c
src/hitlistpool.h
src/intlistpool.c
src/intlistpool.h
src/listpool.c
src/listpool.h
src/pathpool.c
src/pathpool.h
src/transcriptpool.c
src/transcriptpool.h
src/trpathpool.c
src/trpathpool.h
src/uint8listpool.c
src/uint8listpool.h
src/uintlistpool.c
src/uintlistpool.h
src/univcoord.h
src/univdiagpool.c
src/univdiagpool.h
src/vectorpool.c
src/vectorpool.h

2023-04-26 11:47:32 -0700 Removed a comment
src/junction.c

2023-04-26 11:47:14 -0700 Handling the case where splice distance is 0, merging the main and fusion paths instead
src/path-fusion.c

2023-04-26 08:06:56 -0700 In using fusion paths, always copying paths when making a pathpair, and freeing all fusion paths when done
src/pathpair-eval.c

2023-04-26 08:06:19 -0700 In Path_copy, copying fusion_alts instead of getting it from qstart_alts or qend_alts
src/path.c

2023-04-26 08:04:00 -0700 Assigning a value for fusion_alts in Path_copy
src/path.c

2023-04-26 08:03:31 -0700 Freeing existing altsplice before re-assigning one
src/path-fusion.c

2023-04-25 18:03:02 -0700 Added contents to trace information
src/intlistpool.c

2023-04-25 18:02:42 -0700 Fixed a memory leak from the results of outer fusion procedures
src/pathpair-eval.c

2023-04-25 18:02:17 -0700 Passing plusp along with query_compress instead of always using true
src/localdb-read.c

2023-04-25 18:01:44 -0700 Fixed memory leaks for intlistpool in merging the main and fusion endpoints, and for middle_path created by outer fusion procedures
src/path-fusion.c

2023-04-25 16:58:58 -0700 Using new interface to Transcript_remap_intersection
src/gsnap.c

2023-04-25 16:58:43 -0700 Added output of contents to trace information
src/univdiagpool.c

2023-04-25 16:58:12 -0700 Changed incorrect usage of uintlistpool to univcoordlistpool
src/trpath-solve.c

2023-04-25 16:57:47 -0700 Providing correct value to Transcriptpool_free_transcript
src/transcript.c

2023-04-25 16:57:24 -0700 Freeing transcripts in Transcript_remap_intersection
src/transcript-remap.c
src/transcript-remap.h

2023-04-25 16:57:03 -0700 In combine_leftright_paths, prohibiting trimming on 3' end past an insertion
src/path-solve.c

2023-04-25 16:56:23 -0700 Added assertions for consistency between query_compress direction and plusp
src/genomebits_consec.c
src/genomebits_count.c

2023-04-25 16:55:58 -0700 Fixed mixing of newly generated Univdiag_T and existing ones, resulting in memory issues
src/extension-search.c

2023-04-25 08:04:43 -0700 Changed compute_qstart_local and compute_qend_local to return NULL instead of a copy of the original path, to allow caller to decide whether to use the original path or a copy
src/path-solve.c

2023-04-25 07:26:51 -0700 Freeing transcripts and exons from paths
src/concordance.c
src/concordance.h
src/extension-search.c
src/extension-search.h
src/gsnap.c
src/kmer-search.c
src/kmer-search.h
src/path-eval.c
src/path-eval.h
src/path-fusion.c
src/path-solve.c
src/path-solve.h
src/path.c
src/path.h
src/pathpair-eval.c
src/pathpair-eval.h
src/pathpair.c
src/pathpair.h
src/resulthr.c
src/resulthr.h
src/segment-search.c
src/segment-search.h
src/stage1hr-paired.c
src/stage1hr-single.c
src/stage1hr-single.h
src/stage1hr.c
src/stage1hr.h
src/transcript-remap.c
src/transcript.c
src/transcript.h
src/transcriptome-search.c
src/transcriptome-search.h
src/trpath-solve.c
src/trpath-solve.h

2023-04-25 06:10:10 -0700 Fixed a memory leak for hitlistpool
src/stage1hr-paired.c

2023-04-25 06:05:33 -0700 Turning off inner fusions until the procedures can be debugged.  Using Path_filter_pick_sensedir
src/stage1hr-paired.c

2023-04-25 06:04:32 -0700 Implemented Path_filter_pick_sensedir, which does not free paths
src/path.c
src/path.h

2023-04-24 19:05:39 -0700 Fixed an issue where List_append was altering the lists in the Stage1_T objects.  Fixed memory leaks
src/stage1hr-paired.c

2023-04-24 19:04:47 -0700 Ensuring that compute_qstart_local and compute_qend_local return paths different from the original one, and requiring the caller to free the original path
src/path-solve.c

2023-04-24 19:03:32 -0700 Implemented debugging procedure Stage1_list_paths
src/stage1hr.c
src/stage1hr.h

2023-04-24 19:02:47 -0700 Fixed debugging statements
src/splice.c

2023-04-24 19:02:23 -0700 Fixed typos in the function names
src/pathpool.c

2023-04-24 19:02:06 -0700 Fixed a memory leak
src/pathpair-eval.c

2023-04-24 19:01:54 -0700 Fixed Path_free to free circular and junction data.  Implemented Path_copy_list
src/path.c
src/path.h

2023-04-24 19:00:58 -0700 For inner fusions, fixed the univdiagonal to be taken from the fusion path
src/path-fusion.c

2023-04-24 19:00:29 -0700 Added information about contents
src/hitlistpool.c

2023-04-24 10:41:30 -0700 Fixed memory leak for intlist and univcoordlist in combine_leftright_paths
src/path-solve.c

2023-04-24 10:32:22 -0700 Applying Path_filter when the number of paths is too high
src/stage1hr-paired.c

2023-04-24 10:31:59 -0700 Applying MAX_HITS to the number of concordant pairs.  Always copying paths from Path_extend when using them in a concordant pathpair
src/concordance.c

2023-04-24 10:30:34 -0700 Implemented Pathpair_gc
src/pathpair.c
src/pathpair.h

2023-04-24 10:30:05 -0700 Using new interface to Path_trim_qstart to Path_trim_qend
src/path-eval.c
src/pathpair-eval.c

2023-04-24 10:29:11 -0700 Using pop instead of next when trimming segments
src/path-trim.c
src/path-trim.h

2023-04-24 10:26:34 -0700 Added a debugging statement
src/mem.c

2023-04-24 10:25:45 -0700 Fixed typo on macro
src/intlistpool.c

2023-04-24 08:30:54 -0700 Modified debugging statements
src/concordance.c

2023-04-24 08:30:33 -0700 Placing a limit on the number of single-end hits, and applying Path_filter if the limit is exceeded
src/stage1hr-paired.c

2023-04-23 18:35:46 -0700 Added a shortcut to memory check procedures
src/hitlistpool.c
src/intlistpool.c
src/listpool.c
src/pathpool.c
src/transcriptpool.c
src/trpathpool.c
src/uint8listpool.c
src/uintlistpool.c
src/univdiagpool.c

2023-04-23 18:34:43 -0700 Fixed memory leaks from hitlistpool
src/path-solve.c

2023-04-23 17:18:38 -0700 Using tracing interfaces to memory pool procedures
src/altsplice.c
src/concordance.c
src/exon.c
src/exon.h
src/extension-search.c
src/extension-search.h
src/junction.c
src/kmer-search.c
src/list.c
src/list.h
src/path-fusion.c
src/path-print-alignment.c
src/path-print-m8.c
src/path-solve.c
src/path-trim.c
src/path.c
src/pathpair-eval.c
src/pathpair.c
src/segment-search.c
src/stage1hr-paired.c
src/stage1hr-single.c
src/stage1hr.c
src/stage1hr.h
src/transcript-remap.c
src/transcript.c
src/transcriptome-search.c
src/trpath-solve.c
src/trpath.c
src/univcoord.h

2023-04-23 17:17:44 -0700 Enabled tracing of allocation and freeing.  Implemented checks for remaining free cells
src/hitlistpool.c
src/hitlistpool.h
src/intlistpool.c
src/intlistpool.h
src/listpool.c
src/listpool.h
src/pathpool.c
src/pathpool.h
src/transcriptpool.c
src/transcriptpool.h
src/trpathpool.c
src/trpathpool.h
src/uint8listpool.c
src/uint8listpool.h
src/uintlistpool.c
src/uintlistpool.h
src/univdiagpool.c
src/univdiagpool.h

2023-04-23 11:49:06 -0700 Using interfaces to new memory pool procedures
src/altsplice.c
src/altsplice.h
src/concordance.c
src/extension-search.c
src/extension-search.h
src/gsnap.c
src/junction.c
src/junction.h
src/path-eval.c
src/path-fusion.c
src/path-solve.c
src/path-solve.h
src/path.c
src/path.h
src/pathpair-eval.c
src/pathpair.c
src/pathpair.h
src/pathpool.c
src/pathpool.h
src/resulthr.c
src/resulthr.h
src/segment-search.c
src/stage1hr-paired.c
src/stage1hr-single.c
src/stage1hr.c
src/stage1hr.h
src/transcriptpool.c
src/trpath-solve.c
src/trpath.c
src/trpath.h
src/trpathpool.c
src/trpathpool.h
src/univcoord.h
src/univdiagpool.c
src/univdiagpool.h

2023-04-23 11:45:00 -0700 Removed files that are generated by automake and configure
src/Makefile.am
src/Makefile.in

2023-04-23 11:44:20 -0700 Added instructions for a test program for new memory pools
src/Makefile.dna.am

2023-04-22 21:59:57 -0700 Rewrote memory pool procedures to re-use freed objects
src/hitlistpool.c
src/hitlistpool.h
src/intlistpool.c
src/intlistpool.h
src/listpool.c
src/listpool.h
src/pathpool.c
src/pathpool.h
src/transcriptpool.c
src/transcriptpool.h
src/trpathpool.c
src/trpathpool.h
src/uint8listpool.c
src/uint8listpool.h
src/uintlistpool.c
src/uintlistpool.h
src/univdiagpool.c
src/univdiagpool.h

2023-04-22 11:34:04 -0700 Revised for version 2023-04-20
share/index.html

2023-04-22 11:33:14 -0700 Distinguishing between softclip and hardclip in supplemental cigars
src/path-print-sam.c

2023-04-22 11:30:37 -0700 Removed file
ChangeLog

2023-04-21 08:25:05 -0700 In combine_leftright_paths, not allowing a change in endpoints beyond chromosomal bounds
src/path-solve.c

2023-04-21 08:24:35 -0700 Added debugging statements
src/path-trim.c

2023-04-20 17:36:56 -0700 Using new interfaces to Spliceends trimming procedures
src/path-solve.c

2023-04-20 17:36:33 -0700 Using transcriptome_align_p and genome_align_p to control behavior
src/stage1hr-single.c
src/stage1hr-single.h

2023-04-20 17:36:00 -0700 Not performing splicing on circular chromosomes
src/spliceends.c
src/spliceends.h

2023-04-20 17:35:34 -0700 Added option --transcriptome-mode
src/gsnap.c

2023-04-20 08:57:22 -0700 Putting memory allocation and freeing commands for patharray and pathpairarray into the output pool
src/list.c
src/path-eval.c
src/path-print-alignment.c
src/pathpair-eval.c
src/stage1hr-paired.c
src/stage1hr-single.c

2023-04-19 15:28:29 -0700 Requiring trpaths to extend to the ends of the alignment
src/trpath-solve.c

2023-04-19 15:28:02 -0700 Changed test for concordance
src/pathpair.c

2023-04-19 13:41:28 -0700 Using genomiclow and genomichigh, instead of genomicstart and genomicend
src/pathpair.c

2023-04-19 13:39:14 -0700 Using Path_genomiclow and Path_genomichigh procedures instead of genomicstart and genomicend
src/concordance.c
src/path-fusion.c
src/path-print-sam.c

2023-04-19 13:38:03 -0700 Allowing for singlepaths5 and singlepaths3 to form a concordant pathpair
src/stage1hr-paired.c

2023-04-19 13:35:54 -0700 Distinguishing between genomicstart/genomicend and genomiclow/genomichigh
src/path.c
src/path.h

2023-04-19 13:27:18 -0700 Handling the case in EF64_chrbounds where chrnum is the last one
src/ef64.c

2023-04-19 09:23:57 -0700 In computing supplemental MD string, handling the case where fusion_plusp is different from path plusp
src/path-print-sam.c

2023-04-19 09:06:28 -0700 Emitting intron alignments for transcripts
src/transcript-remap.c

2023-04-19 08:44:13 -0700 In paired_read_segment_search, freeing newpairs only if pathpairs are found
src/stage1hr-paired.c

2023-04-19 08:43:02 -0700 In Genomebits_mark_mismatches, considering both segment_plusp and query_plusp
src/genomebits_count.c
src/genomebits_count.h

2023-04-19 08:42:03 -0700 Fixed computation of genomic_diff when fusion_plusp differs from path plusp
src/path-eval.c

2023-04-19 08:41:31 -0700 Fixed debugging statements
src/path-solve.c

2023-04-19 08:41:18 -0700 Fixed coordinates of XT field based on fusion_plusp
src/path-print-sam.c

2023-04-18 15:40:31 -0700 Added share directory for Web site
share/archive.html
share/index.html

2023-04-18 11:24:02 -0700 Removed unused variables and parameters
src/kmer-search.c
src/kmer-search.h
src/path-fusion.c
src/path-fusion.h
src/path-print-alignment.c
src/path-solve.c
src/path-solve.h
src/pathpair-eval.c
src/pathpair-eval.h
src/single-cell.c
src/splice.c
src/splice.h
src/stage1hr-paired.c
src/stage1hr-single.c
src/transcript-remap.c
src/transcript.c
src/transcriptome-search.c
src/uintlistpool.c

2023-04-18 11:22:40 -0700 Hiding unused procedure
src/localdb-read.c

2023-04-18 10:22:20 -0700 Using vectorpool to allocate vectors in Altsplice_T object.  Resolves memory leak
src/altsplice.c
src/altsplice.h
src/concordance.c
src/concordance.h
src/extension-search.c
src/extension-search.h
src/gsnap.c
src/kmer-search.c
src/kmer-search.h
src/path-fusion.c
src/path-fusion.h
src/path-solve.c
src/path-solve.h
src/path.c
src/path.h
src/pathpair-eval.c
src/pathpair-eval.h
src/pathpair.c
src/pathpair.h
src/segment-search.c
src/segment-search.h
src/stage1hr-paired.c
src/stage1hr-paired.h
src/stage1hr-single.c
src/stage1hr-single.h

2023-04-18 07:49:42 -0700 Added comment in help output about --suboptimal-levels
src/gsnap.c

2023-04-18 07:44:44 -0700 Handling the case where querylength < index1part
src/stage1hr-paired.c
src/stage1hr-single.c
src/stage1hr.c

2023-04-17 21:22:13 -0700 Added debugging statements
src/concordance.c

2023-04-17 21:21:59 -0700 Added debugging statements
src/stage1hr-paired.c

2023-04-17 21:21:46 -0700 Fixed usage of mincoverage_filter instead of nmismatches_filter
src/pathpair-eval.c

2023-04-17 19:51:20 -0700 Computing and using min coverage
src/stage1hr-paired.c
src/stage1hr-paired.h
src/stage1hr-single.c
src/stage1hr-single.h

2023-04-17 19:50:53 -0700 Including fusion coverage in Path_coverage
src/path.c

2023-04-17 19:50:36 -0700 Fixed printing of XT field to use sensedir information
src/path-print-sam.c

2023-04-17 19:50:17 -0700 Fixed printing to consider invertp
src/path-print-alignment.c

2023-04-17 19:49:48 -0700 Filtering based on min coverage
src/path-eval.c
src/path-eval.h
src/pathpair-eval.c
src/pathpair-eval.h

2023-04-17 19:49:25 -0700 Added back option --min-coverage
src/gsnap.c

2023-04-17 09:01:00 -0700 Updated for the latest version
VERSION
config.site.rosalind.prd
config.site.rosalind.tst

2023-04-17 08:59:47 -0700 Removed file, which is generated from configure.ac by autoconf
configure

2023-04-17 08:58:05 -0700 Using Transcript_remap_intersection
src/gsnap.c

2023-04-17 08:57:53 -0700 Implemented Transcript_remap_intersection
src/transcript-remap.c
src/transcript-remap.h

2023-04-17 08:57:28 -0700 In standard paths, handling splice_querypos correctly for the minus strand
src/path-fusion.c

2023-04-17 08:57:00 -0700 Handling fusion parts with multiple exons
src/path-print-alignment.c

2023-04-16 18:47:04 -0700 Added shortsplicedist to Path_fusion_setup
src/gsnap.c
src/path-fusion.h

2023-04-16 18:46:44 -0700 Checking fusion paths to see if they should be considered a standard path instead
src/path-fusion.c

2023-04-16 18:45:08 -0700 Implemented Transcript_remap_matchp
src/transcript-remap.c
src/transcript-remap.h

2023-04-16 14:35:10 -0700 Fixed debugging statements
src/transcriptome.c

2023-04-16 14:34:57 -0700 Changing exon coordinates for alignment to be 1-based
src/transcript-remap.c

2023-04-16 14:33:53 -0700 Performing Transcript_remap on fusion alignments
src/gsnap.c

2023-04-16 14:33:19 -0700 Assigning values to fusion dinucleotides in Junction_copy
src/junction.c

2023-04-16 14:32:01 -0700 Fixed assignment of TRANSLOC resulttypes
src/resulthr.c

2023-04-16 14:30:31 -0700 Initializing fusion_endpoints and fusion_invalid_transcripts
src/path.c

2023-04-16 14:30:18 -0700 Added field fusion_invalid_transcripts
src/path.h

2023-04-16 14:29:50 -0700 Removed extraneous XT:Z field.  Printing XX and XY fields for fusion line
src/path-print-sam.c

2023-04-14 22:22:47 -0700 Turning off debugging macro
src/path.c

2023-04-14 22:22:32 -0700 Fixed debugging statements
src/path-eval.c

2023-04-14 22:20:36 -0700 Not checking for sarray8 when determining whether localdb was read successfully
src/localdb-read.c

2023-04-14 22:19:59 -0700 Handling multiple paths returned by single-end fusion procedures
src/stage1hr-single.c

2023-04-14 22:19:33 -0700 Fixed comparison of nmatches with nmismatches allowed for single-end fusion procedures.  Allowing single-end fusion procedures to return multiple paths
src/path-fusion.c
src/path-fusion.h

2023-04-14 21:44:30 -0700 Handling multiple fusion paths returned from outer fusion procedures
src/pathpair-eval.c

2023-04-14 21:43:55 -0700 Fixed check on nmatches vs nmismatches_allowed.  Allowing outer fusion procedures to return multiple fusion paths
src/path-fusion.c
src/path-fusion.h

2023-04-14 04:47:40 -0700 Checking for trdiagonal < querylength
src/transcriptome-search.c

2023-04-14 04:47:05 -0700 In combine_leftright_paths, revising qstart1 for insertions.  Disallowing calls to Splice_resolve when chrnum is circular
src/path-solve.c

2023-04-14 04:45:30 -0700 Revising queryend3 for insertions
src/path-fusion.c

2023-04-13 07:55:38 -0700 Added maintainer files
bootstrap.dna
bootstrap.gsnaptoo
config.site.rosalind.prd
config.site.rosalind.tst
src/Makefile.dna.am
src/Makefile.gsnaptoo.am

2023-04-13 07:39:20 -0700 Allowing for other text in chrsubset file beyond the first word of each line
src/gsnap.c

2023-04-11 17:32:15 -0700 Initial import
AUTHORS
COPYING
ChangeLog
INSTALL
LICENSE
Makefile.am
Makefile.in
NEWS
NOTICE
README
VERSION
acinclude.m4
aclocal.m4
config.site
config/acx_mmap_fixed.m4
config/acx_mmap_variable.m4
config/acx_pthread.m4
config/asm-bsr.m4
config/ax_check_compile_flag.m4
config/ax_compiler_vendor.m4
config/ax_cpuid_intel.m4
config/ax_cpuid_non_intel.m4
config/ax_ext.m4
config/ax_mpi.m4
config/builtin-popcount.m4
config/compile
config/config.guess
config/config.sub
config/depcomp
config/expand.m4
config/fopen.m4
config/install-sh
config/madvise-flags.m4
config/missing
config/mmap-flags.m4
config/pagesize.m4
config/perl.m4
config/shm-flags.m4
config/simd-intrinsics.m4
config/sse2_slli_const_imm8.m4
config/struct-stat64.m4
config/sttni.m4
config/test-driver
configure
configure.ac
src/Makefile.am
src/Makefile.in
src/access.c
src/access.h
src/altsplice.c
src/altsplice.h
src/assert.c
src/assert.h
src/atoi.c
src/atoi.h
src/atoiindex.c
src/bigendian.c
src/bigendian.h
src/bitpack64-access.c
src/bitpack64-access.h
src/bitpack64-incr.c
src/bitpack64-incr.h
src/bitpack64-read.c
src/bitpack64-read.h
src/bitpack64-readtwo.c
src/bitpack64-readtwo.h
src/bitpack64-write.c
src/bitpack64-write.h
src/bitvector.c
src/bitvector.h
src/block.c
src/block.h
src/bool.h
src/boyer-moore.c
src/boyer-moore.h
src/bytecoding.c
src/bytecoding.h
src/bzip2.c
src/bzip2.h
src/cellpool.c
src/cellpool.h
src/changepoint.c
src/changepoint.h
src/chimera.c
src/chimera.h
src/chrnum.c
src/chrnum.h
src/chrom.c
src/chrom.h
src/cmet.c
src/cmet.h
src/cmetindex.c
src/comp.h
src/compare2truth.c
src/complement.h
src/compress-write.c
src/compress-write.h
src/compress.c
src/compress.h
src/concordance.c
src/concordance.h
src/config.h.in
src/cpuid.c
src/cpuid.h
src/datadir.c
src/datadir.h
src/diag.c
src/diag.h
src/diagdef.h
src/diagnostic.c
src/diagnostic.h
src/diagpool.c
src/diagpool.h
src/dinucl_bits.c
src/dinucl_bits.h
src/doublelist.c
src/doublelist.h
src/dynprog.c
src/dynprog.h
src/dynprog_cdna.c
src/dynprog_cdna.h
src/dynprog_end.c
src/dynprog_end.h
src/dynprog_genome.c
src/dynprog_genome.h
src/dynprog_simd.c
src/dynprog_simd.h
src/dynprog_single.c
src/dynprog_single.h
src/ef64.c
src/ef64.h
src/except.c
src/except.h
src/exon.c
src/exon.h
src/extension-search.c
src/extension-search.h
src/fastlog.h
src/filestring.c
src/filestring.h
src/filesuffix.h
src/fopen.c
src/fopen.h
src/gbuffer.c
src/gbuffer.h
src/genome-write.c
src/genome-write.h
src/genome.c
src/genome.h
src/genome_canonical.c
src/genome_canonical.h
src/genome_sites.c
src/genome_sites.h
src/genomebits.c
src/genomebits.h
src/genomebits_consec.c
src/genomebits_consec.h
src/genomebits_count.c
src/genomebits_count.h
src/genomebits_decode.c
src/genomebits_decode.h
src/genomebits_indel.c
src/genomebits_indel.h
src/genomebits_kmer.c
src/genomebits_kmer.h
src/genomebits_mismatches.c
src/genomebits_mismatches.h
src/genomicpos.c
src/genomicpos.h
src/get-genome.c
src/getline.c
src/getline.h
src/getopt.c
src/getopt.h
src/getopt1.c
src/gexact.c
src/gexact_select.c
src/gfilter.c
src/gfilter_select.c
src/gmap.c
src/gmap_select.c
src/gmapindex.c
src/gmapl_select.c
src/gregion.c
src/gregion.h
src/gsnap.c
src/gsnap_select.c
src/gsnapl_select.c
src/hitlistpool.c
src/hitlistpool.h
src/iit-read-univ.c
src/iit-read-univ.h
src/iit-read.c
src/iit-read.h
src/iit-write-univ.c
src/iit-write-univ.h
src/iit-write.c
src/iit-write.h
src/iit_dump.c
src/iit_get.c
src/iit_store.c
src/iitdef.h
src/inbuffer.c
src/inbuffer.h
src/indel.c
src/indel.h
src/indexdb-cat.c
src/indexdb-write.c
src/indexdb-write.h
src/indexdb.c
src/indexdb.h
src/indexdbdef.h
src/intersect-large.c
src/intersect-large.h
src/intersect-simd.c
src/intersect-simd.h
src/intersect-uint2.c
src/intersect-uint2.h
src/intersect.c
src/intersect.h
src/intersectp-simd.c
src/intersectp-simd.h
src/interval.c
src/interval.h
src/intlist.c
src/intlist.h
src/intlistpool.c
src/intlistpool.h
src/intron.c
src/intron.h
src/junction.c
src/junction.h
src/kmer-search.c
src/kmer-search.h
src/knownindels.c
src/knownindels.h
src/knownsplicing.c
src/knownsplicing.h
src/list.c
src/list.h
src/listpool.c
src/listpool.h
src/littleendian.c
src/littleendian.h
src/localdb-read.c
src/localdb-read.h
src/localdb-write.c
src/localdb-write.h
src/mapq.c
src/mapq.h
src/match.c
src/match.h
src/matchdef.h
src/matchpool.c
src/matchpool.h
src/maxent.c
src/maxent.h
src/maxent_hr.c
src/maxent_hr.h
src/md5.c
src/md5.h
src/mem.c
src/mem.h
src/merge-diagonals-heap.c
src/merge-diagonals-heap.h
src/merge-diagonals-simd-uint4.c
src/merge-diagonals-simd-uint4.h
src/merge-diagonals-simd-uint8.c
src/merge-diagonals-simd-uint8.h
src/merge-uint4.c
src/merge-uint4.h
src/merge-uint8.c
src/merge-uint8.h
src/mergeinfo.c
src/mergeinfo.h
src/method.c
src/method.h
src/mode.h
src/nr-x.c
src/nr-x.h
src/oligo.c
src/oligo.h
src/oligoindex_hr.c
src/oligoindex_hr.h
src/orderstat.c
src/orderstat.h
src/outbuffer.c
src/outbuffer.h
src/output.c
src/output.h
src/outputtype.h
src/pair.c
src/pair.h
src/pairdef.h
src/pairpool.c
src/pairpool.h
src/parserange.c
src/parserange.h
src/pass.h
src/path-eval.c
src/path-eval.h
src/path-fusion.c
src/path-fusion.h
src/path-learn.c
src/path-learn.h
src/path-print-alignment.c
src/path-print-alignment.h
src/path-print-m8.c
src/path-print-m8.h
src/path-print-sam.c
src/path-print-sam.h
src/path-solve.c
src/path-solve.h
src/path-trim.c
src/path-trim.h
src/path.c
src/path.h
src/pathpair-eval.c
src/pathpair-eval.h
src/pathpair.c
src/pathpair.h
src/pathpool.c
src/pathpool.h
src/pbinom.c
src/pbinom.h
src/popcount.c
src/popcount.h
src/printbuffer.c
src/printbuffer.h
src/reader.c
src/reader.h
src/record.h
src/request.c
src/request.h
src/result.c
src/result.h
src/resulthr.c
src/resulthr.h
src/saca-k.c
src/saca-k.h
src/sam_sort.c
src/samflags.h
src/samheader.c
src/samheader.h
src/samprint-exact.c
src/samprint-exact.h
src/samread.c
src/samread.h
src/sarray-read.c
src/sarray-read.h
src/sarray-write.c
src/sarray-write.h
src/scores.h
src/sedgesort.c
src/sedgesort.h
src/segment-search.c
src/segment-search.h
src/segmentpos.c
src/segmentpos.h
src/select64-common.c
src/select64-common.h
src/select64-ones.c
src/select64-ones.h
src/select64-zeroes.c
src/select64-zeroes.h
src/semaphore.c
src/semaphore.h
src/sense.h
src/separator.h
src/sequence.c
src/sequence.h
src/shortread.c
src/shortread.h
src/simd.h
src/simde/arm/neon.h
src/simde/arm/neon/aba.h
src/simde/arm/neon/abd.h
src/simde/arm/neon/abdl.h
src/simde/arm/neon/abs.h
src/simde/arm/neon/add.h
src/simde/arm/neon/addhn.h
src/simde/arm/neon/addl.h
src/simde/arm/neon/addl_high.h
src/simde/arm/neon/addlv.h
src/simde/arm/neon/addv.h
src/simde/arm/neon/addw.h
src/simde/arm/neon/addw_high.h
src/simde/arm/neon/and.h
src/simde/arm/neon/bcax.h
src/simde/arm/neon/bic.h
src/simde/arm/neon/bsl.h
src/simde/arm/neon/cage.h
src/simde/arm/neon/cagt.h
src/simde/arm/neon/ceq.h
src/simde/arm/neon/ceqz.h
src/simde/arm/neon/cge.h
src/simde/arm/neon/cgez.h
src/simde/arm/neon/cgt.h
src/simde/arm/neon/cgtz.h
src/simde/arm/neon/cle.h
src/simde/arm/neon/clez.h
src/simde/arm/neon/cls.h
src/simde/arm/neon/clt.h
src/simde/arm/neon/cltz.h
src/simde/arm/neon/clz.h
src/simde/arm/neon/cmla.h
src/simde/arm/neon/cmla_rot180.h
src/simde/arm/neon/cmla_rot270.h
src/simde/arm/neon/cmla_rot90.h
src/simde/arm/neon/cnt.h
src/simde/arm/neon/combine.h
src/simde/arm/neon/create.h
src/simde/arm/neon/cvt.h
src/simde/arm/neon/dot.h
src/simde/arm/neon/dot_lane.h
src/simde/arm/neon/dup_lane.h
src/simde/arm/neon/dup_n.h
src/simde/arm/neon/eor.h
src/simde/arm/neon/ext.h
src/simde/arm/neon/fma.h
src/simde/arm/neon/fma_lane.h
src/simde/arm/neon/fma_n.h
src/simde/arm/neon/get_high.h
src/simde/arm/neon/get_lane.h
src/simde/arm/neon/get_low.h
src/simde/arm/neon/hadd.h
src/simde/arm/neon/hsub.h
src/simde/arm/neon/ld1.h
src/simde/arm/neon/ld1_dup.h
src/simde/arm/neon/ld1_lane.h
src/simde/arm/neon/ld1_x2.h
src/simde/arm/neon/ld1_x3.h
src/simde/arm/neon/ld1_x4.h
src/simde/arm/neon/ld1q_x2.h
src/simde/arm/neon/ld1q_x3.h
src/simde/arm/neon/ld1q_x4.h
src/simde/arm/neon/ld2.h
src/simde/arm/neon/ld3.h
src/simde/arm/neon/ld4.h
src/simde/arm/neon/ld4_lane.h
src/simde/arm/neon/max.h
src/simde/arm/neon/maxnm.h
src/simde/arm/neon/maxv.h
src/simde/arm/neon/min.h
src/simde/arm/neon/minnm.h
src/simde/arm/neon/minv.h
src/simde/arm/neon/mla.h
src/simde/arm/neon/mla_n.h
src/simde/arm/neon/mlal.h
src/simde/arm/neon/mlal_high.h
src/simde/arm/neon/mlal_high_n.h
src/simde/arm/neon/mlal_lane.h
src/simde/arm/neon/mlal_n.h
src/simde/arm/neon/mls.h
src/simde/arm/neon/mls_n.h
src/simde/arm/neon/mlsl.h
src/simde/arm/neon/mlsl_high.h
src/simde/arm/neon/mlsl_high_n.h
src/simde/arm/neon/mlsl_lane.h
src/simde/arm/neon/mlsl_n.h
src/simde/arm/neon/movl.h
src/simde/arm/neon/movl_high.h
src/simde/arm/neon/movn.h
src/simde/arm/neon/movn_high.h
src/simde/arm/neon/mul.h
src/simde/arm/neon/mul_lane.h
src/simde/arm/neon/mul_n.h
src/simde/arm/neon/mull.h
src/simde/arm/neon/mull_high.h
src/simde/arm/neon/mull_lane.h
src/simde/arm/neon/mull_n.h
src/simde/arm/neon/mvn.h
src/simde/arm/neon/neg.h
src/simde/arm/neon/orn.h
src/simde/arm/neon/orr.h
src/simde/arm/neon/padal.h
src/simde/arm/neon/padd.h
src/simde/arm/neon/paddl.h
src/simde/arm/neon/pmax.h
src/simde/arm/neon/pmin.h
src/simde/arm/neon/qabs.h
src/simde/arm/neon/qadd.h
src/simde/arm/neon/qdmulh.h
src/simde/arm/neon/qdmulh_lane.h
src/simde/arm/neon/qdmulh_n.h
src/simde/arm/neon/qdmull.h
src/simde/arm/neon/qmovn.h
src/simde/arm/neon/qmovn_high.h
src/simde/arm/neon/qmovun.h
src/simde/arm/neon/qneg.h
src/simde/arm/neon/qrdmulh.h
src/simde/arm/neon/qrdmulh_lane.h
src/simde/arm/neon/qrdmulh_n.h
src/simde/arm/neon/qrshrn_n.h
src/simde/arm/neon/qrshrun_n.h
src/simde/arm/neon/qshl.h
src/simde/arm/neon/qshlu_n.h
src/simde/arm/neon/qshrn_n.h
src/simde/arm/neon/qshrun_n.h
src/simde/arm/neon/qsub.h
src/simde/arm/neon/qtbl.h
src/simde/arm/neon/qtbx.h
src/simde/arm/neon/rbit.h
src/simde/arm/neon/recpe.h
src/simde/arm/neon/recps.h
src/simde/arm/neon/reinterpret.h
src/simde/arm/neon/rev16.h
src/simde/arm/neon/rev32.h
src/simde/arm/neon/rev64.h
src/simde/arm/neon/rhadd.h
src/simde/arm/neon/rnd.h
src/simde/arm/neon/rndi.h
src/simde/arm/neon/rndm.h
src/simde/arm/neon/rndn.h
src/simde/arm/neon/rndp.h
src/simde/arm/neon/rshl.h
src/simde/arm/neon/rshr_n.h
src/simde/arm/neon/rshrn_n.h
src/simde/arm/neon/rsqrte.h
src/simde/arm/neon/rsqrts.h
src/simde/arm/neon/rsra_n.h
src/simde/arm/neon/set_lane.h
src/simde/arm/neon/shl.h
src/simde/arm/neon/shl_n.h
src/simde/arm/neon/shll_n.h
src/simde/arm/neon/shr_n.h
src/simde/arm/neon/shrn_n.h
src/simde/arm/neon/sqadd.h
src/simde/arm/neon/sra_n.h
src/simde/arm/neon/sri_n.h
src/simde/arm/neon/st1.h
src/simde/arm/neon/st1_lane.h
src/simde/arm/neon/st2.h
src/simde/arm/neon/st2_lane.h
src/simde/arm/neon/st3.h
src/simde/arm/neon/st3_lane.h
src/simde/arm/neon/st4.h
src/simde/arm/neon/st4_lane.h
src/simde/arm/neon/sub.h
src/simde/arm/neon/subhn.h
src/simde/arm/neon/subl.h
src/simde/arm/neon/subl_high.h
src/simde/arm/neon/subw.h
src/simde/arm/neon/subw_high.h
src/simde/arm/neon/tbl.h
src/simde/arm/neon/tbx.h
src/simde/arm/neon/trn.h
src/simde/arm/neon/trn1.h
src/simde/arm/neon/trn2.h
src/simde/arm/neon/tst.h
src/simde/arm/neon/types.h
src/simde/arm/neon/uqadd.h
src/simde/arm/neon/uzp.h
src/simde/arm/neon/uzp1.h
src/simde/arm/neon/uzp2.h
src/simde/arm/neon/xar.h
src/simde/arm/neon/zip.h
src/simde/arm/neon/zip1.h
src/simde/arm/neon/zip2.h
src/simde/check.h
src/simde/debug-trap.h
src/simde/hedley.h
src/simde/simde-align.h
src/simde/simde-arch.h
src/simde/simde-common.h
src/simde/simde-complex.h
src/simde/simde-constify.h
src/simde/simde-detect-clang.h
src/simde/simde-diagnostic.h
src/simde/simde-f16.h
src/simde/simde-features.h
src/simde/simde-math.h
src/simde/x86/avx.h
src/simde/x86/avx2.h
src/simde/x86/avx512.h
src/simde/x86/avx512/2intersect.h
src/simde/x86/avx512/4dpwssd.h
src/simde/x86/avx512/4dpwssds.h
src/simde/x86/avx512/abs.h
src/simde/x86/avx512/add.h
src/simde/x86/avx512/adds.h
src/simde/x86/avx512/and.h
src/simde/x86/avx512/andnot.h
src/simde/x86/avx512/avg.h
src/simde/x86/avx512/bitshuffle.h
src/simde/x86/avx512/blend.h
src/simde/x86/avx512/broadcast.h
src/simde/x86/avx512/cast.h
src/simde/x86/avx512/cmp.h
src/simde/x86/avx512/cmpeq.h
src/simde/x86/avx512/cmpge.h
src/simde/x86/avx512/cmpgt.h
src/simde/x86/avx512/cmple.h
src/simde/x86/avx512/cmplt.h
src/simde/x86/avx512/cmpneq.h
src/simde/x86/avx512/compress.h
src/simde/x86/avx512/conflict.h
src/simde/x86/avx512/copysign.h
src/simde/x86/avx512/cvt.h
src/simde/x86/avx512/cvts.h
src/simde/x86/avx512/cvtt.h
src/simde/x86/avx512/dbsad.h
src/simde/x86/avx512/div.h
src/simde/x86/avx512/dpbf16.h
src/simde/x86/avx512/dpbusd.h
src/simde/x86/avx512/dpbusds.h
src/simde/x86/avx512/dpwssd.h
src/simde/x86/avx512/dpwssds.h
src/simde/x86/avx512/expand.h
src/simde/x86/avx512/extract.h
src/simde/x86/avx512/fixupimm.h
src/simde/x86/avx512/fixupimm_round.h
src/simde/x86/avx512/flushsubnormal.h
src/simde/x86/avx512/fmadd.h
src/simde/x86/avx512/fmsub.h
src/simde/x86/avx512/fnmadd.h
src/simde/x86/avx512/fnmsub.h
src/simde/x86/avx512/insert.h
src/simde/x86/avx512/kshift.h
src/simde/x86/avx512/load.h
src/simde/x86/avx512/loadu.h
src/simde/x86/avx512/lzcnt.h
src/simde/x86/avx512/madd.h
src/simde/x86/avx512/maddubs.h
src/simde/x86/avx512/max.h
src/simde/x86/avx512/min.h
src/simde/x86/avx512/mov.h
src/simde/x86/avx512/mov_mask.h
src/simde/x86/avx512/movm.h
src/simde/x86/avx512/mul.h
src/simde/x86/avx512/mulhi.h
src/simde/x86/avx512/mulhrs.h
src/simde/x86/avx512/mullo.h
src/simde/x86/avx512/multishift.h
src/simde/x86/avx512/negate.h
src/simde/x86/avx512/or.h
src/simde/x86/avx512/packs.h
src/simde/x86/avx512/packus.h
src/simde/x86/avx512/permutex2var.h
src/simde/x86/avx512/permutexvar.h
src/simde/x86/avx512/popcnt.h
src/simde/x86/avx512/range.h
src/simde/x86/avx512/range_round.h
src/simde/x86/avx512/rol.h
src/simde/x86/avx512/rolv.h
src/simde/x86/avx512/ror.h
src/simde/x86/avx512/rorv.h
src/simde/x86/avx512/round.h
src/simde/x86/avx512/roundscale.h
src/simde/x86/avx512/roundscale_round.h
src/simde/x86/avx512/sad.h
src/simde/x86/avx512/scalef.h
src/simde/x86/avx512/set.h
src/simde/x86/avx512/set1.h
src/simde/x86/avx512/set4.h
src/simde/x86/avx512/setone.h
src/simde/x86/avx512/setr.h
src/simde/x86/avx512/setr4.h
src/simde/x86/avx512/setzero.h
src/simde/x86/avx512/shldv.h
src/simde/x86/avx512/shuffle.h
src/simde/x86/avx512/sll.h
src/simde/x86/avx512/slli.h
src/simde/x86/avx512/sllv.h
src/simde/x86/avx512/sqrt.h
src/simde/x86/avx512/sra.h
src/simde/x86/avx512/srai.h
src/simde/x86/avx512/srav.h
src/simde/x86/avx512/srl.h
src/simde/x86/avx512/srli.h
src/simde/x86/avx512/srlv.h
src/simde/x86/avx512/store.h
src/simde/x86/avx512/storeu.h
src/simde/x86/avx512/sub.h
src/simde/x86/avx512/subs.h
src/simde/x86/avx512/ternarylogic.h
src/simde/x86/avx512/test.h
src/simde/x86/avx512/testn.h
src/simde/x86/avx512/types.h
src/simde/x86/avx512/unpackhi.h
src/simde/x86/avx512/unpacklo.h
src/simde/x86/avx512/xor.h
src/simde/x86/avx512/xorsign.h
src/simde/x86/fma.h
src/simde/x86/mmx.h
src/simde/x86/sse.h
src/simde/x86/sse2.h
src/simde/x86/sse3.h
src/simde/x86/sse4.1.h
src/simde/x86/sse4.2.h
src/simde/x86/ssse3.h
src/simde/x86/svml.h
src/simplepair.c
src/simplepair.h
src/single-cell.c
src/single-cell.h
src/smooth.c
src/smooth.h
src/snpindex.c
src/splice.c
src/splice.h
src/spliceends.c
src/spliceends.h
src/spliceendsgen.c
src/spliceendsgen.h
src/splicestringpool.c
src/splicestringpool.h
src/splicetrie.c
src/splicetrie.h
src/splicetrie_build.c
src/splicetrie_build.h
src/stage1.c
src/stage1.h
src/stage1hr-paired.c
src/stage1hr-paired.h
src/stage1hr-single.c
src/stage1hr-single.h
src/stage1hr.c
src/stage1hr.h
src/stage2.c
src/stage2.h
src/stage3.c
src/stage3.h
src/stopwatch.c
src/stopwatch.h
src/table.c
src/table.h
src/tableint.c
src/tableint.h
src/tableuint.c
src/tableuint.h
src/tableuint8.c
src/tableuint8.h
src/transcript-remap.c
src/transcript-remap.h
src/transcript.c
src/transcript.h
src/transcriptome-search.c
src/transcriptome-search.h
src/transcriptome.c
src/transcriptome.h
src/transcriptpool.c
src/transcriptpool.h
src/translation.c
src/translation.h
src/trindex.c
src/trpath-solve.c
src/trpath-solve.h
src/trpath.c
src/trpath.h
src/trpathpool.c
src/trpathpool.h
src/types.h
src/uint8list.c
src/uint8list.h
src/uint8listpool.c
src/uint8listpool.h
src/uint8table.c
src/uint8table.h
src/uint8table_rh.c
src/uint8table_rh.h
src/uint8tableuint.c
src/uint8tableuint.h
src/uintlist.c
src/uintlist.h
src/uintlistpool.c
src/uintlistpool.h
src/uinttable.c
src/uinttable.h
src/uinttable_rh.c
src/uinttable_rh.h
src/uinttableuint.c
src/uinttableuint.h
src/univcoord.h
src/univdiag.c
src/univdiag.h
src/univdiagdef.h
src/univdiagpool.c
src/univdiagpool.h
src/univinterval.c
src/univinterval.h
src/vectorpool.c
src/vectorpool.h
tests/Makefile.am
tests/Makefile.in
tests/align.test.in
tests/align.test.ok
tests/coords1.test.in
tests/coords1.test.ok
tests/defs
tests/fa.iittest
tests/iit.test.in
tests/iit_get.out.ok
tests/iittest.iit.ok
tests/map.test.ok
tests/setup.genomecomp.ok
tests/setup.ref123positions.ok
tests/setup1.test.in
tests/ss.chr17test
tests/ss.her2
util/Makefile.am
util/Makefile.in
util/dbsnp_iit.pl.in
util/ensembl_genes.pl.in
util/fa_coords.pl.in
util/gff3_genes.pl.in
util/gff3_introns.pl.in
util/gff3_splicesites.pl.in
util/gmap_build.pl.in
util/gmap_cat.pl.in
util/gmap_process.pl.in
util/gtf_genes.pl.in
util/gtf_introns.pl.in
util/gtf_splicesites.pl.in
util/gtf_transcript_splicesites.pl.in
util/gvf_iit.pl.in
util/md_coords.pl.in
util/psl_genes.pl.in
util/psl_introns.pl.in
util/psl_splicesites.pl.in
util/vcf_iit.pl.in

2022-10-24 20:06:07 +0200 Initial commit
README.md
