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malex-guest pushed a change to branch upstream
in repository gmap.
from d49f40e New upstream version 2016-11-07
new 67575fa New upstream version 2017-08-15
The 1 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 | 674 +
Makefile.in | 5 +-
VERSION | 2 +-
config/ax_cpuid_intel.m4 | 11 +-
config/ax_cpuid_non_intel.m4 | 37 +-
config/ax_ext.m4 | 70 +-
configure | 957 +-
configure.ac | 222 +-
src/Makefile.am | 109 +-
src/Makefile.in | 7740 +++-
src/block.c | 10 +-
src/chimera.c | 45 +-
src/chimera.h | 5 +-
src/chrom.c | 89 +-
src/cigar.c | 1647 +
src/cigar.h | 33 +
src/config.h.in | 3 -
src/cpuid.c | 46 +-
src/datadir.c | 9 +-
src/diag.c | 96 +-
src/dynprog.c | 13 +-
src/dynprog.h | 3 +-
src/dynprog_cdna.c | 4 +-
src/dynprog_end.c | 53 +-
src/dynprog_end.h | 8 +-
src/dynprog_genome.c | 161 +-
src/dynprog_simd.c | 50 +-
src/dynprog_simd.h | 4 +
src/dynprog_single.c | 7 +-
src/genome.c | 12 +-
src/genome128_hr.c | 11583 +++--
src/genome128_hr.h | 7 +-
src/get-genome.c | 328 +-
src/gmap.c | 1069 +-
src/gmap_select.c | 24 +
src/gmapl_select.c | 24 +
src/gsnap.c | 287 +-
src/gsnap_select.c | 24 +
src/gsnapl_select.c | 24 +
src/iit-read.c | 818 +-
src/iit-read.h | 19 +-
src/iit-write.c | 41 +-
src/iit-write.h | 5 +-
src/iit_get.c | 4 +-
src/indel.c | 125 +-
src/indel.h | 7 +-
src/indexdb.c | 21 +-
src/indexdb_hr.c | 2988 +-
src/interval.c | 66 +-
src/interval.h | 8 +-
src/intlist.c | 23 +-
src/intlist.h | 4 +-
src/intron.c | 43 +-
src/intron.h | 10 +-
src/junction.c | 7 +-
src/list.c | 32 +-
src/list.h | 3 +-
src/littleendian.h | 5 +-
src/maxent_hr.c | 10 +-
src/mem.h | 26 +-
src/merge-heap.c | 400 +
src/merge-heap.h | 19 +
src/merge.c | 1110 +
src/merge.h | 45 +
src/oligoindex_hr.c | 45074 ++++++-------------
src/oligoindex_hr.h | 54 +-
src/outbuffer.c | 121 +-
src/outbuffer.h | 6 +-
src/output.c | 190 +-
src/output.h | 5 +-
src/pair.c | 2804 +-
src/pair.h | 55 +-
src/pairpool.c | 10 +-
src/parserange.c | 9 +-
src/popcount.c | 8 +-
src/popcount.h | 8 +-
src/samflags.h | 3 +-
src/samheader.c | 4 +-
src/samprint.c | 3330 +-
src/samprint.h | 43 +-
src/sarray-read.c | 7486 +--
src/sarray-read.h | 35 +-
src/{sarray-read.c => sarray-search.c} | 2145 +-
src/sarray-search.h | 32 +
src/sequence.c | 36 +-
src/sequence.h | 4 +-
src/shortread.c | 83 +-
src/smooth.c | 35 +-
src/spanningelt.c | 36 +-
src/spanningelt.h | 6 +-
src/stage1hr.c | 3513 +-
src/stage1hr.h | 10 +-
src/stage2.c | 1863 +-
src/stage3.c | 1572 +-
src/stage3.h | 30 +-
src/stage3hr.c | 2378 +-
src/stage3hr.h | 31 +-
src/substring.c | 459 +-
src/substring.h | 55 +-
src/table.c | 28 +-
src/table.h | 4 +-
src/uniqscan.c | 14 +-
tests/Makefile.in | 5 +-
util/Makefile.am | 12 +-
util/Makefile.in | 27 +-
util/gmap_build.pl.in | 66 +-
...ites.pl.in => gtf_transcript_splicesites.pl.in} | 82 +-
107 files changed, 49868 insertions(+), 53237 deletions(-)
create mode 100644 src/cigar.c
create mode 100644 src/cigar.h
create mode 100644 src/merge-heap.c
create mode 100644 src/merge-heap.h
create mode 100644 src/merge.c
create mode 100644 src/merge.h
copy src/{sarray-read.c => sarray-search.c} (82%)
create mode 100644 src/sarray-search.h
copy util/{gtf_splicesites.pl.in => gtf_transcript_splicesites.pl.in} (75%)
mode change 100755 => 100644
--
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