[med-svn] [stacks] 06/07: Merge tag 'upstream/1.46'
Andreas Tille
tille at debian.org
Sat Jun 24 07:04:23 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository stacks.
commit f24f4e983727bdd9a69d011a8ef558f746e963cd
Merge: 55df420 5eedfd9
Author: Andreas Tille <tille at debian.org>
Date: Sat Jun 24 08:21:12 2017 +0200
Merge tag 'upstream/1.46'
Upstream version 1.46
ChangeLog | 34 +
Makefile.am | 47 +-
Makefile.in | 3814 ++++++++++++-----------
aclocal.m4 | 740 ++---
config.h.in | 9 +-
config/compile | 232 +-
config/depcomp | 531 ++--
config/install-sh | 385 +--
config/missing | 461 ++-
config/test-driver | 148 -
configure | 5763 +++++++++++++++++++++--------------
configure.ac | 31 +-
htslib/._INSTALL | Bin 181 -> 0 bytes
htslib/._LICENSE | Bin 181 -> 0 bytes
htslib/._Makefile | Bin 181 -> 0 bytes
htslib/._NEWS | Bin 181 -> 0 bytes
htslib/._README | Bin 181 -> 0 bytes
htslib/._bgzf.c | Bin 181 -> 0 bytes
htslib/._bgzip.c | Bin 181 -> 0 bytes
htslib/._cram | Bin 181 -> 0 bytes
htslib/._faidx.c | Bin 181 -> 0 bytes
htslib/._hfile.c | Bin 181 -> 0 bytes
htslib/._hfile_internal.h | Bin 181 -> 0 bytes
htslib/._hfile_irods.c | Bin 181 -> 0 bytes
htslib/._hfile_libcurl.c | Bin 181 -> 0 bytes
htslib/._hfile_net.c | Bin 181 -> 0 bytes
htslib/._hts.c | Bin 181 -> 0 bytes
htslib/._hts_internal.h | Bin 181 -> 0 bytes
htslib/._htsfile.c | Bin 181 -> 0 bytes
htslib/._htslib | Bin 181 -> 0 bytes
htslib/._htslib.pc.in | Bin 181 -> 0 bytes
htslib/._htslib_vars.mk | Bin 181 -> 0 bytes
htslib/._kfunc.c | Bin 181 -> 0 bytes
htslib/._knetfile.c | Bin 181 -> 0 bytes
htslib/._kstring.c | Bin 181 -> 0 bytes
htslib/._md5.c | Bin 181 -> 0 bytes
htslib/._plugin.c | Bin 181 -> 0 bytes
htslib/._regidx.c | Bin 181 -> 0 bytes
htslib/._sam.c | Bin 181 -> 0 bytes
htslib/._synced_bcf_reader.c | Bin 181 -> 0 bytes
htslib/._tabix.c | Bin 181 -> 0 bytes
htslib/._tbx.c | Bin 181 -> 0 bytes
htslib/._vcf.c | Bin 181 -> 0 bytes
htslib/._vcf_sweep.c | Bin 181 -> 0 bytes
htslib/._vcfutils.c | Bin 181 -> 0 bytes
htslib/cram/._cram.h | Bin 181 -> 0 bytes
htslib/cram/._cram_codecs.c | Bin 181 -> 0 bytes
htslib/cram/._cram_codecs.h | Bin 181 -> 0 bytes
htslib/cram/._cram_decode.c | Bin 181 -> 0 bytes
htslib/cram/._cram_decode.h | Bin 181 -> 0 bytes
htslib/cram/._cram_encode.c | Bin 181 -> 0 bytes
htslib/cram/._cram_encode.h | Bin 181 -> 0 bytes
htslib/cram/._cram_external.c | Bin 181 -> 0 bytes
htslib/cram/._cram_index.c | Bin 181 -> 0 bytes
htslib/cram/._cram_index.h | Bin 181 -> 0 bytes
htslib/cram/._cram_io.c | Bin 181 -> 0 bytes
htslib/cram/._cram_io.h | Bin 181 -> 0 bytes
htslib/cram/._cram_samtools.c | Bin 181 -> 0 bytes
htslib/cram/._cram_samtools.h | Bin 181 -> 0 bytes
htslib/cram/._cram_stats.c | Bin 181 -> 0 bytes
htslib/cram/._cram_stats.h | Bin 181 -> 0 bytes
htslib/cram/._cram_structs.h | Bin 181 -> 0 bytes
htslib/cram/._files.c | Bin 181 -> 0 bytes
htslib/cram/._mFILE.c | Bin 181 -> 0 bytes
htslib/cram/._mFILE.h | Bin 181 -> 0 bytes
htslib/cram/._misc.h | Bin 181 -> 0 bytes
htslib/cram/._open_trace_file.c | Bin 181 -> 0 bytes
htslib/cram/._open_trace_file.h | Bin 181 -> 0 bytes
htslib/cram/._os.h | Bin 181 -> 0 bytes
htslib/cram/._pooled_alloc.c | Bin 181 -> 0 bytes
htslib/cram/._pooled_alloc.h | Bin 181 -> 0 bytes
htslib/cram/._rANS_byte.h | Bin 181 -> 0 bytes
htslib/cram/._rANS_static.c | Bin 181 -> 0 bytes
htslib/cram/._rANS_static.h | Bin 181 -> 0 bytes
htslib/cram/._sam_header.c | Bin 181 -> 0 bytes
htslib/cram/._sam_header.h | Bin 181 -> 0 bytes
htslib/cram/._string_alloc.c | Bin 181 -> 0 bytes
htslib/cram/._string_alloc.h | Bin 181 -> 0 bytes
htslib/cram/._thread_pool.c | Bin 181 -> 0 bytes
htslib/cram/._thread_pool.h | Bin 181 -> 0 bytes
htslib/cram/._vlen.c | Bin 181 -> 0 bytes
htslib/cram/._vlen.h | Bin 181 -> 0 bytes
htslib/cram/._zfio.c | Bin 181 -> 0 bytes
htslib/cram/._zfio.h | Bin 181 -> 0 bytes
htslib/htslib/._bgzf.h | Bin 181 -> 0 bytes
htslib/htslib/._cram.h | Bin 181 -> 0 bytes
htslib/htslib/._faidx.h | Bin 181 -> 0 bytes
htslib/htslib/._hfile.h | Bin 181 -> 0 bytes
htslib/htslib/._hts.h | Bin 181 -> 0 bytes
htslib/htslib/._hts_defs.h | Bin 181 -> 0 bytes
htslib/htslib/._kbitset.h | Bin 181 -> 0 bytes
htslib/htslib/._kfunc.h | Bin 181 -> 0 bytes
htslib/htslib/._khash.h | Bin 181 -> 0 bytes
htslib/htslib/._khash_str2int.h | Bin 181 -> 0 bytes
htslib/htslib/._klist.h | Bin 181 -> 0 bytes
htslib/htslib/._knetfile.h | Bin 181 -> 0 bytes
htslib/htslib/._kseq.h | Bin 181 -> 0 bytes
htslib/htslib/._ksort.h | Bin 181 -> 0 bytes
htslib/htslib/._kstring.h | Bin 181 -> 0 bytes
htslib/htslib/._regidx.h | Bin 181 -> 0 bytes
htslib/htslib/._sam.h | Bin 181 -> 0 bytes
htslib/htslib/._synced_bcf_reader.h | Bin 181 -> 0 bytes
htslib/htslib/._tbx.h | Bin 181 -> 0 bytes
htslib/htslib/._vcf.h | Bin 181 -> 0 bytes
htslib/htslib/._vcf_sweep.h | Bin 181 -> 0 bytes
htslib/htslib/._vcfutils.h | Bin 181 -> 0 bytes
scripts/count_fixed_catalog_snps.py | 323 ++
scripts/denovo_map.pl | 11 +-
scripts/integrate_alignments.py | 1 +
scripts/ref_map.pl | 9 +-
src/BamI.h | 285 +-
src/MetaPopInfo.cc | 43 +-
src/MetaPopInfo.h | 6 +-
src/PopMap.h | 9 +-
src/SamI.h | 356 +--
src/Vcf.cc | 2 +
src/aln_utils.cc | 55 +-
src/aln_utils.h | 2 +-
src/bootstrap.h | 19 +-
src/catalog_utils.cc | 22 +
src/catalog_utils.h | 6 +
src/clone_filter.cc | 2 +
src/constants.cc | 88 +
src/constants.h | 85 +-
src/cstacks.cc | 160 +-
src/estacks.cc | 9 +-
src/export_formats.cc | 169 +-
src/export_formats.h | 2 -
src/file_io.cc | 24 -
src/file_io.h | 1 -
src/genotypes.cc | 13 +-
src/hstacks.cc | 2 +
src/input.cc | 38 +-
src/input.h | 9 +-
src/kmer_filter.cc | 2 +
src/locus.cc | 7 +-
src/log_utils.cc | 15 +
src/log_utils.h | 15 +-
src/mst.cc | 8 +
src/mst.h | 8 +-
src/phasedstacks.cc | 2 +
src/populations.cc | 179 +-
src/populations.h | 2 +
src/process_radtags.cc | 99 +-
src/process_shortreads.cc | 18 +-
src/pstacks.cc | 508 +--
src/pstacks.h | 13 +-
src/renz.cc | 64 +-
src/rxstacks.cc | 77 +-
src/smoothing.h | 22 +-
src/sql_utilities.cc | 6 +-
src/sstacks.cc | 143 +-
src/stacks.h | 8 +-
src/ustacks.cc | 286 +-
src/ustacks.h | 4 +-
src/utils.cc | 36 +-
src/utils.h | 30 +
157 files changed, 8489 insertions(+), 7009 deletions(-)
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