[med-svn] [gmap] branch upstream updated (11ae4ff -> 88e5821)
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri Mar 13 09:51:51 UTC 2015
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a change to branch upstream
in repository gmap.
from 11ae4ff Imported Upstream version 2014-10-22
new 61cf1e5 Imported Upstream version 2014-11-25
new 88e5821 Imported Upstream version 2014-12-23
The 2 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 | 332 ++++++
Makefile.in | 5 +-
README | 25 +-
TODO | 3 -
VERSION | 2 +-
acinclude.m4 | 3 +
config/ax_ext.m4 | 15 +-
config/ax_mpi.m4 | 176 +++
configure | 641 +++++++++-
configure.ac | 65 +-
src/ChangeLog | 0
src/Makefile.in | 5 +-
src/access.c | 42 +-
src/bitpack64-read.c | 30 +-
src/bitpack64-read.h | 4 +
src/bitpack64-readtwo.c | 6 +-
src/bitpack64-write.c | 14 +-
src/bytecoding.c | 69 +-
src/chimera.c | 59 +-
src/chimera.h | 6 +-
src/compress-write.c | 13 +-
src/compress.h | 5 +-
src/config.h.in | 9 +-
src/doublelist.c | 34 +-
src/doublelist.h | 6 +-
src/dynprog.h | 5 +-
src/except.h | 6 +-
src/genome-write.c | 131 ++-
src/genome.c | 32 +-
src/genome128_hr.c | 12 +-
src/genome_sites.c | 170 +--
src/genomicpos.h | 6 +-
src/get-genome.c | 28 +-
src/gmap.c | 182 ++-
src/gmapindex.c | 58 +-
src/gsnap.c | 271 +++--
src/iit-read-univ.c | 107 +-
src/iit-read.c | 200 ++--
src/iit-read.h | 7 +-
src/iit-write-univ.c | 14 +-
src/iit_get.c | 6 +-
src/iit_store.c | 27 +-
src/indel.c | 10 +-
src/indexdb-write.c | 146 ++-
src/indexdb-write.h | 5 +-
src/indexdb.c | 30 +-
src/indexdb.h | 6 +-
src/indexdb_hr.c | 28 +-
src/indexdbdef.h | 5 +-
src/mem.c | 62 +-
src/oligoindex_hr.c | 21 +-
src/oligoindex_hr.h | 9 +-
src/outbuffer.c | 88 +-
src/pair.c | 857 ++++++++++----
src/pair.h | 30 +-
src/popcount.c | 6 +-
src/popcount.h | 5 +-
src/sam_sort.c | 304 ++++-
src/samflags.h | 27 +-
src/samheader.c | 92 +-
src/samheader.h | 6 +-
src/samprint.c | 2572 +++++++++++++++++++++++++++++-----------
src/samprint.h | 15 +-
src/samread.c | 356 +++++-
src/samread.h | 13 +-
src/sarray-read.c | 1137 +++++++++++++-----
src/sequence.h | 7 +-
src/snpindex.c | 22 +-
src/splice.c | 767 +++++++-----
src/stage1.c | 23 +-
src/stage1hr.c | 2733 ++++++++++++++++++++++++++++---------------
src/stage1hr.h | 15 +-
src/stage2.c | 39 +-
src/stage3.c | 586 ++++------
src/stage3.h | 15 +-
src/stage3hr.c | 2163 +++++++++++++++++++---------------
src/stage3hr.h | 33 +-
src/substring.c | 313 +++--
src/substring.h | 17 +-
src/table.c | 20 +-
src/tableuint8.c | 21 +-
src/uniqscan.c | 20 +-
src/univinterval.c | 13 +-
tests/Makefile.in | 3 +
util/Makefile.in | 3 +
util/gff3_genes.pl.in | 5 +-
util/gff3_introns.pl.in | 5 +-
util/gff3_splicesites.pl.in | 5 +-
util/gmap_build.pl.in | 4 +-
89 files changed, 10497 insertions(+), 4996 deletions(-)
delete mode 100644 TODO
create mode 100755 config/ax_mpi.m4
delete mode 100644 src/ChangeLog
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gmap.git
More information about the debian-med-commit
mailing list