[med-svn] [stacks] 02/03: Merge tag 'upstream/1.42'
Andreas Tille
tille at debian.org
Sat Aug 13 09:04:17 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository stacks.
commit 7100acd0cd1ed14a73dbd64236603a8d0164055a
Merge: c0ff32a df2c72a
Author: Andreas Tille <tille at debian.org>
Date: Sat Aug 13 10:49:24 2016 +0200
Merge tag 'upstream/1.42'
Upstream version 1.42
ChangeLog | 23 +
Makefile.am | 28 +-
Makefile.in | 548 +-
README | 33 +-
configure | 54 +-
configure.ac | 25 +-
htslib/._INSTALL | Bin 0 -> 181 bytes
htslib/._LICENSE | Bin 0 -> 181 bytes
htslib/._Makefile | Bin 0 -> 181 bytes
htslib/._NEWS | Bin 0 -> 181 bytes
htslib/._README | Bin 0 -> 181 bytes
htslib/._bgzf.c | Bin 0 -> 181 bytes
htslib/._bgzip.c | Bin 0 -> 181 bytes
htslib/._cram | Bin 0 -> 181 bytes
htslib/._faidx.c | Bin 0 -> 181 bytes
htslib/._hfile.c | Bin 0 -> 181 bytes
htslib/._hfile_internal.h | Bin 0 -> 181 bytes
htslib/._hfile_irods.c | Bin 0 -> 181 bytes
htslib/._hfile_libcurl.c | Bin 0 -> 181 bytes
htslib/._hfile_net.c | Bin 0 -> 181 bytes
htslib/._hts.c | Bin 0 -> 181 bytes
htslib/._hts_internal.h | Bin 0 -> 181 bytes
htslib/._htsfile.c | Bin 0 -> 181 bytes
htslib/._htslib | Bin 0 -> 181 bytes
htslib/._htslib.pc.in | Bin 0 -> 181 bytes
htslib/._htslib_vars.mk | Bin 0 -> 181 bytes
htslib/._kfunc.c | Bin 0 -> 181 bytes
htslib/._knetfile.c | Bin 0 -> 181 bytes
htslib/._kstring.c | Bin 0 -> 181 bytes
htslib/._md5.c | Bin 0 -> 181 bytes
htslib/._plugin.c | Bin 0 -> 181 bytes
htslib/._regidx.c | Bin 0 -> 181 bytes
htslib/._sam.c | Bin 0 -> 181 bytes
htslib/._synced_bcf_reader.c | Bin 0 -> 181 bytes
htslib/._tabix.c | Bin 0 -> 181 bytes
htslib/._tbx.c | Bin 0 -> 181 bytes
htslib/._vcf.c | Bin 0 -> 181 bytes
htslib/._vcf_sweep.c | Bin 0 -> 181 bytes
htslib/._vcfutils.c | Bin 0 -> 181 bytes
htslib/INSTALL | 102 +
htslib/LICENSE | 69 +
htslib/Makefile | 426 ++
htslib/NEWS | 109 +
htslib/README | 5 +
htslib/bgzf.c | 1330 +++++
htslib/bgzip.c | 311 ++
htslib/cram/._cram.h | Bin 0 -> 181 bytes
htslib/cram/._cram_codecs.c | Bin 0 -> 181 bytes
htslib/cram/._cram_codecs.h | Bin 0 -> 181 bytes
htslib/cram/._cram_decode.c | Bin 0 -> 181 bytes
htslib/cram/._cram_decode.h | Bin 0 -> 181 bytes
htslib/cram/._cram_encode.c | Bin 0 -> 181 bytes
htslib/cram/._cram_encode.h | Bin 0 -> 181 bytes
htslib/cram/._cram_external.c | Bin 0 -> 181 bytes
htslib/cram/._cram_index.c | Bin 0 -> 181 bytes
htslib/cram/._cram_index.h | Bin 0 -> 181 bytes
htslib/cram/._cram_io.c | Bin 0 -> 181 bytes
htslib/cram/._cram_io.h | Bin 0 -> 181 bytes
htslib/cram/._cram_samtools.c | Bin 0 -> 181 bytes
htslib/cram/._cram_samtools.h | Bin 0 -> 181 bytes
htslib/cram/._cram_stats.c | Bin 0 -> 181 bytes
htslib/cram/._cram_stats.h | Bin 0 -> 181 bytes
htslib/cram/._cram_structs.h | Bin 0 -> 181 bytes
htslib/cram/._files.c | Bin 0 -> 181 bytes
htslib/cram/._mFILE.c | Bin 0 -> 181 bytes
htslib/cram/._mFILE.h | Bin 0 -> 181 bytes
htslib/cram/._misc.h | Bin 0 -> 181 bytes
htslib/cram/._open_trace_file.c | Bin 0 -> 181 bytes
htslib/cram/._open_trace_file.h | Bin 0 -> 181 bytes
htslib/cram/._os.h | Bin 0 -> 181 bytes
htslib/cram/._pooled_alloc.c | Bin 0 -> 181 bytes
htslib/cram/._pooled_alloc.h | Bin 0 -> 181 bytes
htslib/cram/._rANS_byte.h | Bin 0 -> 181 bytes
htslib/cram/._rANS_static.c | Bin 0 -> 181 bytes
htslib/cram/._rANS_static.h | Bin 0 -> 181 bytes
htslib/cram/._sam_header.c | Bin 0 -> 181 bytes
htslib/cram/._sam_header.h | Bin 0 -> 181 bytes
htslib/cram/._string_alloc.c | Bin 0 -> 181 bytes
htslib/cram/._string_alloc.h | Bin 0 -> 181 bytes
htslib/cram/._thread_pool.c | Bin 0 -> 181 bytes
htslib/cram/._thread_pool.h | Bin 0 -> 181 bytes
htslib/cram/._vlen.c | Bin 0 -> 181 bytes
htslib/cram/._vlen.h | Bin 0 -> 181 bytes
htslib/cram/._zfio.c | Bin 0 -> 181 bytes
htslib/cram/._zfio.h | Bin 0 -> 181 bytes
htslib/cram/cram.h | 61 +
htslib/cram/cram_codecs.c | 1950 +++++++
htslib/cram/cram_codecs.h | 194 +
htslib/cram/cram_decode.c | 3159 +++++++++++
htslib/cram/cram_decode.h | 112 +
htslib/cram/cram_encode.c | 3105 +++++++++++
htslib/cram/cram_encode.h | 105 +
htslib/cram/cram_external.c | 377 ++
htslib/cram/cram_index.c | 582 +++
htslib/cram/cram_index.h | 99 +
htslib/cram/cram_io.c | 4604 ++++++++++++++++
htslib/cram/cram_io.h | 669 +++
htslib/cram/cram_samtools.c | 149 +
htslib/cram/cram_samtools.h | 105 +
htslib/cram/cram_stats.c | 448 ++
htslib/cram/cram_stats.h | 59 +
htslib/cram/cram_structs.h | 821 +++
htslib/cram/files.c | 74 +
htslib/cram/mFILE.c | 694 +++
htslib/cram/mFILE.h | 89 +
htslib/cram/misc.h | 110 +
htslib/cram/open_trace_file.c | 414 ++
htslib/cram/open_trace_file.h | 125 +
htslib/cram/os.h | 308 ++
htslib/cram/pooled_alloc.c | 188 +
htslib/cram/pooled_alloc.h | 64 +
htslib/cram/rANS_byte.h | 336 ++
htslib/cram/rANS_static.c | 868 ++++
htslib/cram/rANS_static.h | 51 +
htslib/cram/sam_header.c | 1268 +++++
htslib/cram/sam_header.h | 459 ++
htslib/cram/string_alloc.c | 155 +
htslib/cram/string_alloc.h | 68 +
htslib/cram/thread_pool.c | 757 +++
htslib/cram/thread_pool.h | 218 +
htslib/cram/vlen.c | 430 ++
htslib/cram/vlen.h | 48 +
htslib/cram/zfio.c | 183 +
htslib/cram/zfio.h | 62 +
htslib/faidx.c | 525 ++
htslib/hfile.c | 751 +++
htslib/hfile_internal.h | 139 +
htslib/hfile_irods.c | 259 +
htslib/hfile_libcurl.c | 917 ++++
htslib/hfile_net.c | 112 +
htslib/hts.c | 2066 ++++++++
htslib/hts_internal.h | 90 +
htslib/htsfile.c | 234 +
htslib/htslib.pc.in | 10 +
htslib/htslib/._bgzf.h | Bin 0 -> 181 bytes
htslib/htslib/._cram.h | Bin 0 -> 181 bytes
htslib/htslib/._faidx.h | Bin 0 -> 181 bytes
htslib/htslib/._hfile.h | Bin 0 -> 181 bytes
htslib/htslib/._hts.h | Bin 0 -> 181 bytes
htslib/htslib/._hts_defs.h | Bin 0 -> 181 bytes
htslib/htslib/._kbitset.h | Bin 0 -> 181 bytes
htslib/htslib/._kfunc.h | Bin 0 -> 181 bytes
htslib/htslib/._khash.h | Bin 0 -> 181 bytes
htslib/htslib/._khash_str2int.h | Bin 0 -> 181 bytes
htslib/htslib/._klist.h | Bin 0 -> 181 bytes
htslib/htslib/._knetfile.h | Bin 0 -> 181 bytes
htslib/htslib/._kseq.h | Bin 0 -> 181 bytes
htslib/htslib/._ksort.h | Bin 0 -> 181 bytes
htslib/htslib/._kstring.h | Bin 0 -> 181 bytes
htslib/htslib/._regidx.h | Bin 0 -> 181 bytes
htslib/htslib/._sam.h | Bin 0 -> 181 bytes
htslib/htslib/._synced_bcf_reader.h | Bin 0 -> 181 bytes
htslib/htslib/._tbx.h | Bin 0 -> 181 bytes
htslib/htslib/._vcf.h | Bin 0 -> 181 bytes
htslib/htslib/._vcf_sweep.h | Bin 0 -> 181 bytes
htslib/htslib/._vcfutils.h | Bin 0 -> 181 bytes
htslib/htslib/bgzf.h | 335 ++
htslib/htslib/cram.h | 492 ++
htslib/htslib/faidx.h | 137 +
htslib/htslib/hfile.h | 215 +
htslib/htslib/hts.h | 639 +++
htslib/htslib/hts_defs.h | 72 +
htslib/htslib/kbitset.h | 160 +
htslib/htslib/kfunc.h | 83 +
htslib/htslib/khash.h | 627 +++
htslib/htslib/khash_str2int.h | 133 +
htslib/htslib/klist.h | 135 +
htslib/htslib/knetfile.h | 101 +
htslib/htslib/kseq.h | 253 +
htslib/htslib/ksort.h | 285 +
htslib/htslib/kstring.h | 277 +
htslib/htslib/regidx.h | 154 +
htslib/htslib/sam.h | 454 ++
htslib/htslib/synced_bcf_reader.h | 302 ++
htslib/htslib/tbx.h | 79 +
htslib/htslib/vcf.h | 914 ++++
htslib/htslib/vcf_sweep.h | 47 +
htslib/htslib/vcfutils.h | 134 +
htslib/htslib_vars.mk | 49 +
htslib/kfunc.c | 282 +
htslib/knetfile.c | 634 +++
htslib/kstring.c | 276 +
htslib/md5.c | 386 ++
htslib/plugin.c | 171 +
htslib/regidx.c | 340 ++
htslib/sam.c | 2073 ++++++++
htslib/synced_bcf_reader.c | 1284 +++++
htslib/tabix.c | 544 ++
htslib/tbx.c | 333 ++
htslib/vcf.c | 3483 +++++++++++++
htslib/vcf_sweep.c | 183 +
htslib/vcfutils.c | 691 +++
scripts/ref_map.pl | 2 +-
src/BamI.h | 41 +-
src/BamUnalignedI.h | 35 +-
src/BowtieI.h | 4 +-
src/GappedAln.h | 6 +-
src/MetaPopInfo.cc | 347 ++
src/MetaPopInfo.h | 111 +
src/PopMap.h | 247 +-
src/PopSum.h | 146 +-
src/SamI.h | 4 +-
src/Tsv.h | 2 +-
src/Vcf.cc | 506 ++
src/Vcf.h | 467 ++
src/aln_utils.cc | 7 +-
src/catalog_utils.cc | 58 +-
src/catalog_utils.h | 44 +
src/clone_filter.cc | 1336 ++---
src/cstacks.cc | 38 +-
src/export_formats.cc | 3333 ++++++++++++
src/export_formats.h | 70 +
src/file_io.cc | 3 +-
...ype_dictionaries.h => genotype_dictionaries.cc} | 224 +-
src/genotype_dictionaries.h | 558 +-
src/genotypes.cc | 110 +-
src/input.cc | 4 +-
src/kmers.cc | 2 +-
src/locus.cc | 2 +-
src/mstack.cc | 4 +-
src/ordered.h | 26 +-
src/populations.cc | 5484 ++++----------------
src/populations.h | 131 +-
src/pstacks.cc | 904 ++--
src/{renz.h => renz.cc} | 119 +-
src/renz.h | 219 +-
src/rxstacks.cc | 136 +-
src/smoothing.h | 13 +-
src/smoothing_utils.h | 4 +-
src/sql_utilities.cc | 299 ++
src/sql_utilities.h | 305 +-
src/sstacks.cc | 16 +-
src/stacks.h | 6 +-
src/ustacks.cc | 8 +-
234 files changed, 56367 insertions(+), 7505 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/stacks.git
More information about the debian-med-commit
mailing list