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
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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
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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
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src/simde/arm/neon/rndp.h
src/simde/arm/neon/rshl.h
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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
