[med-svn] [Git][med-team/gmap][master] 9 commits: New upstream version 2025-07-31+ds

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / gmap


Commits:
20ba7fb5 by Étienne Mollier at 2025-10-03T20:53:12+02:00
New upstream version 2025-07-31+ds
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15089250 by Étienne Mollier at 2025-10-03T20:53:19+02:00
Update upstream source from tag 'upstream/2025-07-31+ds'

Update to upstream version '2025-07-31+ds'
with Debian dir 2e5ccc5095f94f5933a9b190a069527c7e04c237
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f8f9c1d9 by Étienne Mollier at 2025-10-03T20:56:08+02:00
simd_fixes: refresh the patch.

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da53cd9f by Étienne Mollier at 2025-10-03T20:56:49+02:00
c23.patch: delete: it is applied upstream.

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f1fb0fb3 by Étienne Mollier at 2025-10-03T20:57:12+02:00
d/copyright: remove unnecessarily excluded file.

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09d08ebe by Étienne Mollier at 2025-10-03T20:57:36+02:00
d/control: declare compliance to standards version 4.7.2.

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a2f86aa0 by Étienne Mollier at 2025-10-03T20:57:55+02:00
d/control: drop redundant Rules-Requires-Root: no.

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ab8e3f1a by Étienne Mollier at 2025-10-03T20:58:53+02:00
d/watch: convert to watch file version 5.

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d41ea062 by Étienne Mollier at 2025-10-03T21:14:22+02:00
d/changelog: ready for upload to unstable.

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298 changed files:

- ChangeLog
- VERSION
- configure.ac
- debian/changelog
- debian/control
- debian/copyright
- − debian/patches/c23.patch
- debian/patches/series
- debian/patches/simd_fixes
- debian/watch
- 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/-/compare/1e84e1791658df5f8b7ca9ec5b5648828f90291c...d41ea062cff2b607326fe1e81be15283ce7b0e56

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View it on GitLab: https://salsa.debian.org/med-team/gmap/-/compare/1e84e1791658df5f8b7ca9ec5b5648828f90291c...d41ea062cff2b607326fe1e81be15283ce7b0e56
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