[med-svn] [stacks] branch upstream updated (7773661 -> df2c72a)
Andreas Tille
tille at debian.org
Sat Aug 13 09:04:18 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository stacks.
from 7773661 Imported Upstream version 1.40
new df2c72a Imported Upstream version 1.42
The 1 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 +-
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(-)
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
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