[med-svn] [gmap] 02/06: Merge tag 'upstream/2014-06-10'
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Tue Jul 1 16:33:14 UTC 2014
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository gmap.
commit 7841a1d95f1845984eaef125fded46c2b669a12b
Merge: b793dbc eff24d5
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Mon Jun 30 13:03:44 2014 +0200
Merge tag 'upstream/2014-06-10'
Upstream version 2014-06-10
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 +-
config/ax_gcc_x86_avx_xgetbv.m4 | 79 +
config/madvise-flags.m4 | 9 +
config/popcnt.m4 | 42 -
config/sse2_shift_defect.m4 | 26 +
configure | 3216 +-
configure.ac | 34 +-
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/ensembl_genes.pl.in | 54 +
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 +
191 files changed, 166843 insertions(+), 109118 deletions(-)
--
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