Étienne Mollier pushed to branch upstream at Debian Med / gmap
Commits: 20ba7fb5 by Étienne Mollier at 2025-10-03T20:53:12+02:00 New upstream version 2025-07-31+ds - - - - - 291 changed files: - ChangeLog - VERSION - configure.ac - 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-write.c - src/bitpack64-write.h - src/block.c - src/block.h - src/bool.h - src/boyer-moore.c - src/boyer-moore.h - src/bytecoding.c - src/bytecoding.h - src/bzip2.c - src/bzip2.h - src/cellpool.c - src/cellpool.h - src/changepoint.c - src/changepoint.h - src/chimera.c - src/chimera.h - src/chrnum.c - src/chrnum.h - src/chrom.c - src/chrom.h - src/cmet.c - src/cmet.h - src/cmetindex.c - src/comp.h - src/complement.h - src/compress-write.c - src/compress-write.h - src/concordance.c - src/concordance.h - src/cpuid.c - src/cpuid.h - src/datadir.c - src/datadir.h - src/diag.c - src/diag.h - src/diagdef.h - src/diagnostic.c - src/diagnostic.h - src/diagpool.c - src/diagpool.h - src/doublelist.c - src/doublelist.h - src/dynprog.c - src/dynprog.h - src/dynprog_cdna.c - src/dynprog_cdna.h - src/dynprog_end.c - src/dynprog_end.h - src/dynprog_genome.c - src/dynprog_genome.h - src/dynprog_simd.c - src/dynprog_single.c - src/dynprog_single.h - src/except.c - src/except.h - src/extension-search.c - src/extension-search.h - src/filestring.c - src/filestring.h - src/filesuffix.h - src/fopen.c - src/gbuffer.c - src/gbuffer.h - src/genome-write.c - src/genome-write.h - src/genome.h - src/genome_sites.c - src/genomebits_count.c - src/genomebits_indel.c - src/genomebits_mismatches.c - src/genomebits_trim.c - src/genomicpos.c - src/genomicpos.h - src/get-genome.c - src/getline.c - src/gmap.c - src/gmapindex.c - src/gregion.c - src/gregion.h - src/gsnap.c - src/hitlistpool.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/indexdb-cat.c - src/indexdb-write.c - src/indexdb-write.h - src/indexdb.h - src/indexdbdef.h - src/intersect-small.c - src/interval.c - src/interval.h - src/intlist.c - src/intlist.h - src/intron.c - src/intron.h - src/junction.c - src/junction.h - src/kmer-search.c - src/knownindels.h - src/knownsplicing.c - src/knownsplicing.h - src/list.c - src/list.h - src/littleendian.c - src/littleendian.h - src/localdb-read.c - src/localdb-read.h - src/mapq.c - src/mapq.h - src/match.c - src/match.h - src/matchdef.h - src/matchpool.c - src/matchpool.h - src/maxent.c - src/maxent_hr.c - src/maxent_hr.h - src/md5.c - src/md5.h - src/mem.c - src/mem.h - src/merge-diagonals-heap-uint4.c - src/merge-diagonals-heap-uint4.h - src/merge-diagonals-heap-uint8.c - src/merge-diagonals-heap-uint8.h - src/merge-diagonals-simd-uint4.c - src/merge-diagonals-simd-uint4.h - src/merge-diagonals-simd-uint8.c - src/merge-diagonals-simd-uint8.h - src/merge-method.h - src/merge-uint4.c - src/merge-uint4.h - src/merge-uint8.c - src/merge-uint8.h - src/mergeinfo.c - src/mode.h - src/oligoindex_hr.c - src/oligoindex_hr.h - src/orderstat.c - src/orderstat.h - src/outbuffer.c - src/pair.c - src/pair.h - src/pairdef.h - src/pairpool.c - src/pairpool.h - src/parserange.c - src/parserange.h - src/path-eval.c - src/path-eval.h - src/path-fusion.c - src/path-fusion.h - src/path-learn.c - src/path-print-alignment.c - src/path-print-sam.c - 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/pathstore.c - src/pathstore.h - src/pbinom.c - src/pbinom.h - src/popcount.c - src/popcount.h - src/reader.c - src/reader.h - src/repair.c - src/request.c - src/request.h - src/result.c - src/result.h - src/samflags.h - src/samheader.c - src/samheader.h - src/sarray-write.c - src/sarray-write.h - src/scores.h - src/segmentpos.c - src/segmentpos.h - src/semaphore.c - src/semaphore.h - src/separator.h - src/sequence.c - src/sequence.h - src/shortread.c - src/shortread.h - src/simplepair.c - src/simplepair.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/splicestringpool.c - src/splicestringpool.h - src/splicetrie.c - src/splicetrie.h - src/splicetrie_build.c - 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.h - src/stopwatch.h - src/support.c - src/table.c - src/table.h - src/tableint.c - src/tableint.h - src/tableuint.h - src/tableuint8.c - src/tableuint8.h - src/tr-extension-search.c - src/tr-extension-search.h - src/transcript-remap.c - src/transcript.c - src/transcriptome-search.c - src/transcriptome.c - src/transcriptome.h - src/trindex.c - src/trpath-convert.c - src/trpath-convert.h - src/trpath-eval.c - src/trpath-eval.h - src/trpath-solve.c - src/trpath-solve.h - src/trpath.c - src/uint8list.c - src/uint8list.h - src/uintlist.c - src/uintlist.h - src/univcoord.h - src/univdiag.c - src/univdiag.h - src/univdiagpool.c - src/univdiagpool.h - src/vectorpool.c - util/Makefile.am - + util/gff3_exons.pl.in - util/gmap_build.pl.in - util/gmap_cat.pl.in - + util/gtf_exons.pl.in The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/gmap/-/commit/20ba7fb5b33765d1dece96d1c40effc81ea24fc7 -- View it on GitLab: https://salsa.debian.org/med-team/gmap/-/commit/20ba7fb5b33765d1dece96d1c40effc81ea24fc7 You're receiving this email because of your account on salsa.debian.org.
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