[med-svn] [gmap] branch upstream updated (15c4dbd -> 1f0c49c)
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Sat Aug 22 06:26:05 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 15c4dbd Imported Upstream version 2014-12-29
new 9c2f1c4 Imported Upstream version 2015-06-10
new 1f0c49c Imported Upstream version 2015-07-23
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 | 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 +-
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 +-
176 files changed, 63630 insertions(+), 38046 deletions(-)
create mode 100644 TODO
create mode 100644 config/shm-flags.m4
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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