[med-svn] [gmap] branch master updated (b793dbc -> 787e0bb)
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Tue Jul 1 16:33:10 UTC 2014
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a change to branch master
in repository gmap.
from b793dbc Move debian/upstream to debian/upstream/metadata
new eff24d5 Imported Upstream version 2014-06-10
new 7841a1d Merge tag 'upstream/2014-06-10'
new 17edede d/changelog: New upstream release
new 5c03bcb debian/patches/install-data-local: refreshed
new 547600c d/control: use canonical Vcs fields - updated Standards-Version - added help2man to Build-Depends: - remove trailing slash from Homepage d/rules: install symlinks for gmap,gsnap in /usr/bin/ - use as bindir /usr/lib/gmap - generate map pages with help of help2man d/install: removed as all files are installed in /usr/lib/gmap/
new 787e0bb d/changelog: updated d/control: added myself to Uploaders:
The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
ChangeLog | 2272 +-
Makefile.am | 4 +-
Makefile.in | 13 +-
NOTICE | 85 +
README | 458 +-
TODO | 3 +
VERSION | 2 +-
acinclude.m4 | 3 +-
config/acx_mmap_fixed.m4 | 4 +-
config/acx_mmap_variable.m4 | 4 +-
config/ax_ext.m4 | 181 +-
...x_gcc_x86_cpuid.m4 => ax_gcc_x86_avx_xgetbv.m4} | 54 +-
config/madvise-flags.m4 | 9 +
config/popcnt.m4 | 42 -
config/sse2_shift_defect.m4 | 26 +
configure | 3216 +-
configure.ac | 34 +-
debian/changelog | 16 +
debian/control | 14 +-
debian/install | 24 -
debian/patches/install-data-local | 10 +-
debian/rules | 24 +-
src/Makefile.am | 167 +-
src/Makefile.in | 2954 +-
src/access.c | 160 +-
src/atoiindex.c | 608 +-
src/bitpack64-access.c | 2135 +
src/bitpack64-access.h | 9 +
src/bitpack64-read.c | 14517 ++++
src/bitpack64-read.h | 30 +
src/bitpack64-readtwo.c | 14242 ++++
src/bitpack64-readtwo.h | 15 +
src/bitpack64-write.c | 5447 ++
src/bitpack64-write.h | 24 +
src/boyer-moore.c | 49 +-
src/bytecoding.c | 785 +
src/bytecoding.h | 53 +
src/{diagpool.c => cellpool.c} | 134 +-
src/cellpool.h | 40 +
src/chimera.c | 359 +-
src/chimera.h | 20 +-
src/chrom.c | 15 +-
src/chrom.h | 6 +-
src/chrsubset.c | 490 -
src/chrsubset.h | 43 -
src/cmetindex.c | 609 +-
src/compress-write.c | 689 +
src/{compress.h => compress-write.h} | 28 +-
src/compress.c | 2629 +-
src/compress.h | 44 +-
src/config.h.in | 45 +-
src/diag.c | 112 +-
src/diag.h | 10 +-
src/diagpool.c | 4 +-
src/doublelist.c | 154 +
src/doublelist.h | 24 +
src/dynprog.c | 11066 +--
src/dynprog.h | 361 +-
src/dynprog_cdna.c | 1321 +
src/dynprog_cdna.h | 32 +
src/dynprog_end.c | 3202 +
src/dynprog_end.h | 117 +
src/dynprog_genome.c | 3900 +
src/dynprog_genome.h | 35 +
src/dynprog_simd.c | 4928 ++
src/dynprog_simd.h | 121 +
src/dynprog_single.c | 1375 +
src/dynprog_single.h | 57 +
src/fastlog.h | 124 +
src/genome-write.c | 40 +-
src/genome-write.h | 13 +-
src/genome.c | 726 +-
src/genome.h | 25 +-
src/genome128_hr.c | 23774 ++++++
src/genome128_hr.h | 76 +
src/genome_hr.c | 71664 -------------------
src/genome_hr.h | 146 -
src/genome_sites.c | 26262 +++++++
src/genome_sites.h | 49 +
src/genomicpos.c | 11 +-
src/genomicpos.h | 10 +-
src/get-genome.c | 248 +-
src/gmap.c | 2684 +-
src/gmapindex.c | 701 +-
src/goby.c | 8 +-
src/goby.h | 4 +-
src/gregion.c | 98 +-
src/gsnap.c | 883 +-
src/iit-read-univ.c | 36 +-
src/iit-read.c | 686 +-
src/iit-read.h | 23 +-
src/iit-write-univ.c | 2 +-
src/iit-write-univ.h | 8 +-
src/iit-write.c | 96 +-
src/iit-write.h | 8 +-
src/iit_get.c | 522 +-
src/iit_store.c | 133 +-
src/iitdef.h | 24 +-
src/inbuffer.c | 53 +-
src/indel.c | 340 +
src/indel.h | 30 +
src/indexdb-write.c | 2111 +-
src/indexdb-write.h | 78 +-
src/indexdb.c | 1842 +-
src/indexdb.h | 88 +-
src/indexdb_hr.c | 412 +-
src/indexdbdef.h | 41 +-
src/interval.c | 35 +-
src/interval.h | 6 +-
src/intlist.c | 22 +-
src/intlist.h | 4 +-
src/littleendian.c | 12 +-
src/littleendian.h | 8 +-
src/mapq.c | 22 +-
src/mapq.h | 8 +-
src/mem.c | 205 +-
src/mem.h | 18 +-
src/oligo.c | 164 +-
src/oligoindex.c | 2020 -
src/oligoindex.h | 106 -
src/oligoindex_hr.c | 7884 +-
src/oligoindex_hr.h | 54 +-
src/outbuffer.c | 1230 +-
src/outbuffer.h | 22 +-
src/pair.c | 422 +-
src/pair.h | 28 +-
src/pairdef.h | 5 +-
src/pairpool.c | 515 +-
src/pairpool.h | 28 +-
src/popcount.c | 4116 ++
src/popcount.h | 18 +
src/resulthr.c | 3 +-
src/saca-k.c | 509 +
src/saca-k.h | 10 +
src/samflags.h | 29 +-
src/samheader.c | 52 +
src/samheader.h | 14 +
src/samprint.c | 2133 +-
src/samprint.h | 55 +-
src/sarray-read.c | 3736 +
src/sarray-read.h | 45 +
src/sarray-write.c | 1588 +
src/sarray-write.h | 54 +
src/scores.h | 10 +-
src/segmentpos.c | 19 +-
src/segmentpos.h | 4 +-
src/sequence.c | 134 +-
src/sequence.h | 8 +-
src/shortread.c | 648 +-
src/shortread.h | 20 +-
src/smooth.c | 576 +-
src/smooth.h | 6 +-
src/snpindex.c | 328 +-
src/spanningelt.c | 339 +-
src/spanningelt.h | 31 +-
src/splice.c | 1628 +
src/splice.h | 65 +
src/splicestringpool.c | 223 +
src/splicestringpool.h | 38 +
src/splicetrie.c | 159 +-
src/splicetrie.h | 10 +-
src/splicetrie_build.c | 1593 +-
src/splicetrie_build.h | 12 +-
src/stage1.c | 318 +-
src/stage1.h | 9 +-
src/stage1hr.c | 13415 ++--
src/stage1hr.h | 40 +-
src/stage2.c | 4411 +-
src/stage2.h | 68 +-
src/stage3.c | 6488 +-
src/stage3.h | 96 +-
src/stage3hr.c | 3873 +-
src/stage3hr.h | 152 +-
src/stopwatch.c | 18 +-
src/substring.c | 649 +-
src/substring.h | 47 +-
src/table.c | 21 +-
src/table.h | 4 +-
src/translation.c | 31 +-
src/types.h | 39 +-
src/uint8list.c | 20 +-
src/uint8list.h | 4 +-
src/uintlist.c | 20 +-
src/uintlist.h | 4 +-
src/uniqscan.c | 267 +-
src/univinterval.c | 63 +-
src/univinterval.h | 13 +-
tests/Makefile.in | 7 +-
util/Makefile.am | 33 +-
util/Makefile.in | 71 +-
util/{psl_genes.pl.in => ensembl_genes.pl.in} | 31 +-
util/fa_coords.pl.in | 96 +-
util/gmap_build.pl.in | 379 +-
util/gmap_process.pl.in | 19 +-
util/gmap_setup.pl.in | 459 -
util/gvf_iit.pl.in | 63 +
196 files changed, 166805 insertions(+), 109196 deletions(-)
create mode 100644 NOTICE
create mode 100644 TODO
copy config/{ax_gcc_x86_cpuid.m4 => ax_gcc_x86_avx_xgetbv.m4} (57%)
delete mode 100644 config/popcnt.m4
create mode 100644 config/sse2_shift_defect.m4
delete mode 100644 debian/install
create mode 100644 src/bitpack64-access.c
create mode 100644 src/bitpack64-access.h
create mode 100644 src/bitpack64-read.c
create mode 100644 src/bitpack64-read.h
create mode 100644 src/bitpack64-readtwo.c
create mode 100644 src/bitpack64-readtwo.h
create mode 100644 src/bitpack64-write.c
create mode 100644 src/bitpack64-write.h
create mode 100644 src/bytecoding.c
create mode 100644 src/bytecoding.h
copy src/{diagpool.c => cellpool.c} (51%)
create mode 100644 src/cellpool.h
delete mode 100644 src/chrsubset.c
delete mode 100644 src/chrsubset.h
create mode 100644 src/compress-write.c
copy src/{compress.h => compress-write.h} (51%)
create mode 100644 src/doublelist.c
create mode 100644 src/doublelist.h
create mode 100644 src/dynprog_cdna.c
create mode 100644 src/dynprog_cdna.h
create mode 100644 src/dynprog_end.c
create mode 100644 src/dynprog_end.h
create mode 100644 src/dynprog_genome.c
create mode 100644 src/dynprog_genome.h
create mode 100644 src/dynprog_simd.c
create mode 100644 src/dynprog_simd.h
create mode 100644 src/dynprog_single.c
create mode 100644 src/dynprog_single.h
create mode 100755 src/fastlog.h
create mode 100644 src/genome128_hr.c
create mode 100644 src/genome128_hr.h
delete mode 100644 src/genome_hr.c
delete mode 100644 src/genome_hr.h
create mode 100644 src/genome_sites.c
create mode 100644 src/genome_sites.h
create mode 100644 src/indel.c
create mode 100644 src/indel.h
delete mode 100644 src/oligoindex.c
delete mode 100644 src/oligoindex.h
create mode 100644 src/popcount.c
create mode 100644 src/popcount.h
create mode 100644 src/saca-k.c
create mode 100644 src/saca-k.h
create mode 100644 src/samheader.c
create mode 100644 src/samheader.h
create mode 100644 src/sarray-read.c
create mode 100644 src/sarray-read.h
create mode 100644 src/sarray-write.c
create mode 100644 src/sarray-write.h
create mode 100644 src/splice.c
create mode 100644 src/splice.h
create mode 100644 src/splicestringpool.c
create mode 100644 src/splicestringpool.h
copy util/{psl_genes.pl.in => ensembl_genes.pl.in} (55%)
delete mode 100755 util/gmap_setup.pl.in
create mode 100755 util/gvf_iit.pl.in
--
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