[med-svn] [stacks] branch master updated (c0ff32a -> 3cc7810)
Andreas Tille
tille at debian.org
Sat Aug 13 09:04:16 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository stacks.
from c0ff32a Add Python depencency since new tool in Python was included by upstream
adds 7773661 Imported Upstream version 1.40
new df2c72a Imported Upstream version 1.42
new 7100acd Merge tag 'upstream/1.42'
new 3cc7810 New upstream version, does not build with -pie hardening option so this is removed
The 3 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 | 23 +
Makefile.am | 28 +-
Makefile.in | 548 +-
README | 33 +-
configure | 54 +-
configure.ac | 25 +-
debian/changelog | 7 +
debian/rules | 3 +-
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 +-
236 files changed, 56376 insertions(+), 7506 deletions(-)
create mode 100644 htslib/._INSTALL
create mode 100644 htslib/._LICENSE
create mode 100644 htslib/._Makefile
create mode 100644 htslib/._NEWS
create mode 100644 htslib/._README
create mode 100644 htslib/._bgzf.c
create mode 100644 htslib/._bgzip.c
create mode 100755 htslib/._cram
create mode 100644 htslib/._faidx.c
create mode 100644 htslib/._hfile.c
create mode 100644 htslib/._hfile_internal.h
create mode 100644 htslib/._hfile_irods.c
create mode 100644 htslib/._hfile_libcurl.c
create mode 100644 htslib/._hfile_net.c
create mode 100644 htslib/._hts.c
create mode 100644 htslib/._hts_internal.h
create mode 100644 htslib/._htsfile.c
create mode 100755 htslib/._htslib
create mode 100644 htslib/._htslib.pc.in
create mode 100644 htslib/._htslib_vars.mk
create mode 100644 htslib/._kfunc.c
create mode 100644 htslib/._knetfile.c
create mode 100644 htslib/._kstring.c
create mode 100644 htslib/._md5.c
create mode 100644 htslib/._plugin.c
create mode 100644 htslib/._regidx.c
create mode 100644 htslib/._sam.c
create mode 100644 htslib/._synced_bcf_reader.c
create mode 100644 htslib/._tabix.c
create mode 100644 htslib/._tbx.c
create mode 100644 htslib/._vcf.c
create mode 100644 htslib/._vcf_sweep.c
create mode 100644 htslib/._vcfutils.c
create mode 100644 htslib/INSTALL
create mode 100644 htslib/LICENSE
create mode 100644 htslib/Makefile
create mode 100644 htslib/NEWS
create mode 100644 htslib/README
create mode 100644 htslib/bgzf.c
create mode 100644 htslib/bgzip.c
create mode 100644 htslib/cram/._cram.h
create mode 100644 htslib/cram/._cram_codecs.c
create mode 100644 htslib/cram/._cram_codecs.h
create mode 100644 htslib/cram/._cram_decode.c
create mode 100644 htslib/cram/._cram_decode.h
create mode 100644 htslib/cram/._cram_encode.c
create mode 100644 htslib/cram/._cram_encode.h
create mode 100644 htslib/cram/._cram_external.c
create mode 100644 htslib/cram/._cram_index.c
create mode 100644 htslib/cram/._cram_index.h
create mode 100644 htslib/cram/._cram_io.c
create mode 100644 htslib/cram/._cram_io.h
create mode 100644 htslib/cram/._cram_samtools.c
create mode 100644 htslib/cram/._cram_samtools.h
create mode 100644 htslib/cram/._cram_stats.c
create mode 100644 htslib/cram/._cram_stats.h
create mode 100644 htslib/cram/._cram_structs.h
create mode 100644 htslib/cram/._files.c
create mode 100644 htslib/cram/._mFILE.c
create mode 100644 htslib/cram/._mFILE.h
create mode 100644 htslib/cram/._misc.h
create mode 100644 htslib/cram/._open_trace_file.c
create mode 100644 htslib/cram/._open_trace_file.h
create mode 100644 htslib/cram/._os.h
create mode 100644 htslib/cram/._pooled_alloc.c
create mode 100644 htslib/cram/._pooled_alloc.h
create mode 100644 htslib/cram/._rANS_byte.h
create mode 100644 htslib/cram/._rANS_static.c
create mode 100644 htslib/cram/._rANS_static.h
create mode 100644 htslib/cram/._sam_header.c
create mode 100644 htslib/cram/._sam_header.h
create mode 100644 htslib/cram/._string_alloc.c
create mode 100644 htslib/cram/._string_alloc.h
create mode 100644 htslib/cram/._thread_pool.c
create mode 100644 htslib/cram/._thread_pool.h
create mode 100644 htslib/cram/._vlen.c
create mode 100644 htslib/cram/._vlen.h
create mode 100644 htslib/cram/._zfio.c
create mode 100644 htslib/cram/._zfio.h
create mode 100644 htslib/cram/cram.h
create mode 100644 htslib/cram/cram_codecs.c
create mode 100644 htslib/cram/cram_codecs.h
create mode 100644 htslib/cram/cram_decode.c
create mode 100644 htslib/cram/cram_decode.h
create mode 100644 htslib/cram/cram_encode.c
create mode 100644 htslib/cram/cram_encode.h
create mode 100644 htslib/cram/cram_external.c
create mode 100644 htslib/cram/cram_index.c
create mode 100644 htslib/cram/cram_index.h
create mode 100644 htslib/cram/cram_io.c
create mode 100644 htslib/cram/cram_io.h
create mode 100644 htslib/cram/cram_samtools.c
create mode 100644 htslib/cram/cram_samtools.h
create mode 100644 htslib/cram/cram_stats.c
create mode 100644 htslib/cram/cram_stats.h
create mode 100644 htslib/cram/cram_structs.h
create mode 100644 htslib/cram/files.c
create mode 100644 htslib/cram/mFILE.c
create mode 100644 htslib/cram/mFILE.h
create mode 100644 htslib/cram/misc.h
create mode 100644 htslib/cram/open_trace_file.c
create mode 100644 htslib/cram/open_trace_file.h
create mode 100644 htslib/cram/os.h
create mode 100644 htslib/cram/pooled_alloc.c
create mode 100644 htslib/cram/pooled_alloc.h
create mode 100644 htslib/cram/rANS_byte.h
create mode 100644 htslib/cram/rANS_static.c
create mode 100644 htslib/cram/rANS_static.h
create mode 100644 htslib/cram/sam_header.c
create mode 100644 htslib/cram/sam_header.h
create mode 100644 htslib/cram/string_alloc.c
create mode 100644 htslib/cram/string_alloc.h
create mode 100644 htslib/cram/thread_pool.c
create mode 100644 htslib/cram/thread_pool.h
create mode 100644 htslib/cram/vlen.c
create mode 100644 htslib/cram/vlen.h
create mode 100644 htslib/cram/zfio.c
create mode 100644 htslib/cram/zfio.h
create mode 100644 htslib/faidx.c
create mode 100644 htslib/hfile.c
create mode 100644 htslib/hfile_internal.h
create mode 100644 htslib/hfile_irods.c
create mode 100644 htslib/hfile_libcurl.c
create mode 100644 htslib/hfile_net.c
create mode 100644 htslib/hts.c
create mode 100644 htslib/hts_internal.h
create mode 100644 htslib/htsfile.c
create mode 100644 htslib/htslib.pc.in
create mode 100644 htslib/htslib/._bgzf.h
create mode 100644 htslib/htslib/._cram.h
create mode 100644 htslib/htslib/._faidx.h
create mode 100644 htslib/htslib/._hfile.h
create mode 100644 htslib/htslib/._hts.h
create mode 100644 htslib/htslib/._hts_defs.h
create mode 100644 htslib/htslib/._kbitset.h
create mode 100644 htslib/htslib/._kfunc.h
create mode 100644 htslib/htslib/._khash.h
create mode 100644 htslib/htslib/._khash_str2int.h
create mode 100644 htslib/htslib/._klist.h
create mode 100644 htslib/htslib/._knetfile.h
create mode 100644 htslib/htslib/._kseq.h
create mode 100644 htslib/htslib/._ksort.h
create mode 100644 htslib/htslib/._kstring.h
create mode 100644 htslib/htslib/._regidx.h
create mode 100644 htslib/htslib/._sam.h
create mode 100644 htslib/htslib/._synced_bcf_reader.h
create mode 100644 htslib/htslib/._tbx.h
create mode 100644 htslib/htslib/._vcf.h
create mode 100644 htslib/htslib/._vcf_sweep.h
create mode 100644 htslib/htslib/._vcfutils.h
create mode 100644 htslib/htslib/bgzf.h
create mode 100644 htslib/htslib/cram.h
create mode 100644 htslib/htslib/faidx.h
create mode 100644 htslib/htslib/hfile.h
create mode 100644 htslib/htslib/hts.h
create mode 100644 htslib/htslib/hts_defs.h
create mode 100644 htslib/htslib/kbitset.h
create mode 100644 htslib/htslib/kfunc.h
create mode 100644 htslib/htslib/khash.h
create mode 100644 htslib/htslib/khash_str2int.h
create mode 100644 htslib/htslib/klist.h
create mode 100644 htslib/htslib/knetfile.h
create mode 100644 htslib/htslib/kseq.h
create mode 100644 htslib/htslib/ksort.h
create mode 100644 htslib/htslib/kstring.h
create mode 100644 htslib/htslib/regidx.h
create mode 100644 htslib/htslib/sam.h
create mode 100644 htslib/htslib/synced_bcf_reader.h
create mode 100644 htslib/htslib/tbx.h
create mode 100644 htslib/htslib/vcf.h
create mode 100644 htslib/htslib/vcf_sweep.h
create mode 100644 htslib/htslib/vcfutils.h
create mode 100644 htslib/htslib_vars.mk
create mode 100644 htslib/kfunc.c
create mode 100644 htslib/knetfile.c
create mode 100644 htslib/kstring.c
create mode 100644 htslib/md5.c
create mode 100644 htslib/plugin.c
create mode 100644 htslib/regidx.c
create mode 100644 htslib/sam.c
create mode 100644 htslib/synced_bcf_reader.c
create mode 100644 htslib/tabix.c
create mode 100644 htslib/tbx.c
create mode 100644 htslib/vcf.c
create mode 100644 htslib/vcf_sweep.c
create mode 100644 htslib/vcfutils.c
create mode 100644 src/MetaPopInfo.cc
create mode 100644 src/MetaPopInfo.h
create mode 100644 src/Vcf.cc
create mode 100644 src/Vcf.h
create mode 100644 src/export_formats.cc
create mode 100644 src/export_formats.h
copy src/{genotype_dictionaries.h => genotype_dictionaries.cc} (75%)
copy src/{renz.h => renz.cc} (80%)
create mode 100644 src/sql_utilities.cc
--
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