[med-svn] [gmap] branch master updated (19b0eb5 -> 02c26bc)
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Sat Aug 22 06:25:56 UTC 2015
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a change to branch master
in repository gmap.
from 19b0eb5 d/patches: refresh patches
new 9c2f1c4 Imported Upstream version 2015-06-10
new dce2678 Merge tag 'upstream/2015-06-10'
new 05bbd32 d/patches: refresh
new 846da4e d/changelog: squash changelog entries
new 1bd109c d/rules: use mkdir -p to create man page dirs d/control: add help2man Build-dep d/gmap.1: removed d/manpages: removed gmap.1
new 1f7e8d4 d/rules: update, use help2man to generate the man page d/gsnap.1: deleted d/mapnages: delete gsnap.1
new 0db8341 d/filter.pl: add regexps to brush up gmap manpages after using help2man d/manpages: deleted d/gmap_build.1: deleted use help2man instead d/rules: add help2man stanza for gsnap and gmap_build
new 1f0c49c Imported Upstream version 2015-07-23
new c277578 Merge tag 'upstream/2015-07-23'
new a3a5fd8 d/changelog: update d/patches/install-data-local: refresh and remove obsoleted patches
new 02c26bc d/changelog: upload to unstable d/control,copyright,docs: applied wrap-and-sort
The 11 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 | 1144 +-
Makefile.am | 2 +-
Makefile.in | 9 +-
README | 40 +-
TODO | 3 +
VERSION | 2 +-
acinclude.m4 | 1 +
config.site | 5 +
config/ax_mpi.m4 | 8 +-
config/shm-flags.m4 | 18 +
configure | 291 +-
configure.ac | 77 +-
debian/changelog | 17 +-
debian/control | 7 +-
debian/copyright | 75 +-
debian/docs | 4 +-
debian/filter.pl | 26 +-
debian/gmap.1 | 405 -
debian/gmap_build.1 | 101 -
debian/gsnap.1 | 514 -
debian/manpages | 3 -
debian/patches/drop_tests_i386.patch | 20 -
debian/patches/fix-big-endian-build.patch | 20 -
debian/patches/install-data-local | 2 +-
debian/patches/series | 1 -
debian/rules | 22 +-
mpi/Makefile.am | 111 +
mpi/Makefile.in | 2042 +++
NEWS => src/ChangeLog | 0
src/Makefile.am | 51 +-
src/Makefile.in | 658 +-
src/access.c | 515 +-
src/access.h | 23 +-
src/atoi.h | 1 +
src/atoiindex.c | 45 +-
src/bigendian.c | 528 +-
src/bigendian.h | 30 +-
src/bitpack64-access.c | 712 +-
src/bitpack64-read.c | 4234 +++---
src/bitpack64-readtwo.c | 4128 +++---
src/bitpack64-write.h | 5 +-
src/block.h | 3 +-
src/bool.h | 6 +-
src/boyer-moore.h | 3 +-
src/bytecoding.c | 154 +-
src/bytecoding.h | 6 +-
src/bzip2.h | 3 +-
src/chimera.c | 32 +-
src/chimera.h | 7 +-
src/chrom.h | 3 +-
src/cmet.h | 1 +
src/cmetindex.c | 40 +-
src/compress.c | 317 +-
src/compress.h | 8 +-
src/config.h.in | 30 +-
src/datadir.h | 3 +-
src/diag.c | 94 +-
src/diag.h | 14 +-
src/diagdef.h | 3 +-
src/diagpool.c | 25 +-
src/diagpool.h | 6 +-
src/doublelist.c | 13 +-
src/doublelist.h | 4 +-
src/dynprog.h | 2 +-
src/dynprog_genome.c | 50 +-
src/except.h | 2 +-
src/filestring.c | 490 +
src/filestring.h | 62 +
src/fopen.h | 2 +-
src/genome-write.c | 6 +-
src/genome-write.h | 3 +-
src/genome.c | 227 +-
src/genome.h | 13 +-
src/genome128_hr.c | 2273 ++--
src/genome128_hr.h | 6 +-
src/genome_sites.h | 3 +-
src/genomicpos.c | 43 +-
src/genomicpos.h | 13 +-
src/get-genome.c | 125 +-
src/gmap.c | 1807 ++-
src/gmapindex.c | 161 +-
src/goby.c | 345 -
src/goby.h | 49 -
src/gregion.h | 3 +-
src/gsnap.c | 2003 ++-
src/iit-read-univ.c | 161 +-
src/iit-read-univ.h | 24 +-
src/iit-read.c | 35 +-
src/iit-read.h | 7 +-
src/iit-write-univ.h | 3 +-
src/iit-write.h | 3 +-
src/iitdef.h | 4 +-
src/inbuffer.c | 969 +-
src/inbuffer.h | 89 +-
src/indel.c | 323 +-
src/indel.h | 23 +-
src/indexdb-write.c | 69 +-
src/indexdb-write.h | 6 +-
src/indexdb.c | 262 +-
src/indexdb.h | 11 +-
src/indexdb_hr.c | 18 +-
src/indexdb_hr.h | 3 +-
src/indexdbdef.h | 12 +-
src/interval.h | 3 +-
src/intlist.c | 44 +-
src/intlist.h | 7 +-
src/intron.h | 3 +-
src/junction.c | 240 +
src/junction.h | 63 +
src/list.c | 12 +-
src/list.h | 4 +-
src/littleendian.h | 4 +-
src/master.c | 510 +
src/master.h | 65 +
src/match.h | 3 +-
src/matchdef.h | 3 +-
src/matchpool.h | 3 +-
src/maxent_hr.h | 2 +
src/md5.c | 6 +-
src/md5.h | 5 +-
src/mem.c | 135 +-
src/mem.h | 7 +-
src/mode.h | 4 +-
src/mpidebug.c | 129 +
src/mpidebug.h | 51 +
src/oligo.h | 3 +-
src/oligoindex_hr.c | 19739 ++++++++++++++++++++--------
src/oligoindex_hr.h | 26 +-
src/outbuffer.c | 3200 ++---
src/outbuffer.h | 81 +-
src/output.c | 972 ++
src/output.h | 57 +
src/pair.c | 1718 +--
src/pair.h | 90 +-
src/pairdef.h | 3 +-
src/parserange.h | 2 +
src/popcount.c | 2 +-
src/popcount.h | 2 +-
src/reader.h | 3 +-
src/request.c | 9 +-
src/request.h | 3 +-
src/resulthr.c | 19 +-
src/resulthr.h | 15 +-
src/sam_sort.c | 684 +-
src/samflags.h | 116 +-
src/samheader.c | 314 +-
src/samheader.h | 32 +-
src/samprint.c | 6603 +++-------
src/samprint.h | 65 +-
src/sarray-read.c | 6298 +++++++--
src/sarray-read.h | 21 +-
src/sarray-write.c | 267 +-
src/sarray-write.h | 6 +-
src/segmentpos.c | 35 +-
src/segmentpos.h | 7 +-
src/sequence.c | 132 +-
src/sequence.h | 32 +-
src/shortread.c | 2713 +++-
src/shortread.h | 151 +-
src/snpindex.c | 81 +-
src/splice.c | 739 +-
src/splice.h | 38 +-
src/stage1.c | 2 +-
src/stage1.h | 3 +-
src/stage1hr.c | 15837 ++++++++++++----------
src/stage1hr.h | 13 +-
src/stage2.c | 156 +-
src/stage2.h | 15 +-
src/stage3.c | 1898 ++-
src/stage3.h | 94 +-
src/stage3hr.c | 9874 +++++++-------
src/stage3hr.h | 136 +-
src/substring.c | 2198 +++-
src/substring.h | 176 +-
src/tableuint8.h | 3 +-
src/translation.c | 42 +-
src/translation.h | 7 +-
src/types.h | 20 +-
src/uint8list.c | 37 +-
src/uint8list.h | 6 +-
src/uintlist.c | 37 +-
src/uintlist.h | 6 +-
src/uniqscan.c | 155 +-
src/univdiag.c | 116 +
src/univdiag.h | 31 +
src/univdiagdef.h | 22 +
src/univinterval.h | 7 +-
tests/Makefile.in | 5 +-
util/Makefile.in | 5 +-
util/gmap_build.pl.in | 26 +-
190 files changed, 63723 insertions(+), 39170 deletions(-)
create mode 100644 TODO
create mode 100644 config/shm-flags.m4
delete mode 100644 debian/gmap.1
delete mode 100644 debian/gmap_build.1
delete mode 100644 debian/gsnap.1
delete mode 100644 debian/manpages
delete mode 100644 debian/patches/drop_tests_i386.patch
delete mode 100644 debian/patches/fix-big-endian-build.patch
create mode 100644 mpi/Makefile.am
create mode 100644 mpi/Makefile.in
copy NEWS => src/ChangeLog (100%)
create mode 100644 src/filestring.c
create mode 100644 src/filestring.h
delete mode 100644 src/goby.c
delete mode 100644 src/goby.h
create mode 100644 src/junction.c
create mode 100644 src/junction.h
create mode 100644 src/master.c
create mode 100644 src/master.h
create mode 100644 src/mpidebug.c
create mode 100644 src/mpidebug.h
create mode 100644 src/output.c
create mode 100644 src/output.h
create mode 100644 src/univdiag.c
create mode 100644 src/univdiag.h
create mode 100644 src/univdiagdef.h
--
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