[med-svn] [stacks] branch master updated (05da8e5 -> e42a401)
Andreas Tille
tille at debian.org
Sat Jun 24 07:04:22 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository stacks.
from 05da8e5 Upload to unstable
new 7aed47a New upstream version
new 41ae540 Standards-Version: 4.0.0 (no changes needed)
new ae43eca do not disable PIE
new 55df420 d/rules: use DEB_SOURCE
new 5eedfd9 New upstream version 1.46
new f24f4e9 Merge tag 'upstream/1.46'
new e42a401 Upload to unstable
The 7 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 | 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 +-
debian/changelog | 10 +
debian/control | 2 +-
debian/rules | 15 +-
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 +
160 files changed, 8507 insertions(+), 7018 deletions(-)
delete mode 100755 config/test-driver
delete mode 100644 htslib/._INSTALL
delete mode 100644 htslib/._LICENSE
delete mode 100644 htslib/._Makefile
delete mode 100644 htslib/._NEWS
delete mode 100644 htslib/._README
delete mode 100644 htslib/._bgzf.c
delete mode 100644 htslib/._bgzip.c
delete mode 100755 htslib/._cram
delete mode 100644 htslib/._faidx.c
delete mode 100644 htslib/._hfile.c
delete mode 100644 htslib/._hfile_internal.h
delete mode 100644 htslib/._hfile_irods.c
delete mode 100644 htslib/._hfile_libcurl.c
delete mode 100644 htslib/._hfile_net.c
delete mode 100644 htslib/._hts.c
delete mode 100644 htslib/._hts_internal.h
delete mode 100644 htslib/._htsfile.c
delete mode 100755 htslib/._htslib
delete mode 100644 htslib/._htslib.pc.in
delete mode 100644 htslib/._htslib_vars.mk
delete mode 100644 htslib/._kfunc.c
delete mode 100644 htslib/._knetfile.c
delete mode 100644 htslib/._kstring.c
delete mode 100644 htslib/._md5.c
delete mode 100644 htslib/._plugin.c
delete mode 100644 htslib/._regidx.c
delete mode 100644 htslib/._sam.c
delete mode 100644 htslib/._synced_bcf_reader.c
delete mode 100644 htslib/._tabix.c
delete mode 100644 htslib/._tbx.c
delete mode 100644 htslib/._vcf.c
delete mode 100644 htslib/._vcf_sweep.c
delete mode 100644 htslib/._vcfutils.c
delete mode 100644 htslib/cram/._cram.h
delete mode 100644 htslib/cram/._cram_codecs.c
delete mode 100644 htslib/cram/._cram_codecs.h
delete mode 100644 htslib/cram/._cram_decode.c
delete mode 100644 htslib/cram/._cram_decode.h
delete mode 100644 htslib/cram/._cram_encode.c
delete mode 100644 htslib/cram/._cram_encode.h
delete mode 100644 htslib/cram/._cram_external.c
delete mode 100644 htslib/cram/._cram_index.c
delete mode 100644 htslib/cram/._cram_index.h
delete mode 100644 htslib/cram/._cram_io.c
delete mode 100644 htslib/cram/._cram_io.h
delete mode 100644 htslib/cram/._cram_samtools.c
delete mode 100644 htslib/cram/._cram_samtools.h
delete mode 100644 htslib/cram/._cram_stats.c
delete mode 100644 htslib/cram/._cram_stats.h
delete mode 100644 htslib/cram/._cram_structs.h
delete mode 100644 htslib/cram/._files.c
delete mode 100644 htslib/cram/._mFILE.c
delete mode 100644 htslib/cram/._mFILE.h
delete mode 100644 htslib/cram/._misc.h
delete mode 100644 htslib/cram/._open_trace_file.c
delete mode 100644 htslib/cram/._open_trace_file.h
delete mode 100644 htslib/cram/._os.h
delete mode 100644 htslib/cram/._pooled_alloc.c
delete mode 100644 htslib/cram/._pooled_alloc.h
delete mode 100644 htslib/cram/._rANS_byte.h
delete mode 100644 htslib/cram/._rANS_static.c
delete mode 100644 htslib/cram/._rANS_static.h
delete mode 100644 htslib/cram/._sam_header.c
delete mode 100644 htslib/cram/._sam_header.h
delete mode 100644 htslib/cram/._string_alloc.c
delete mode 100644 htslib/cram/._string_alloc.h
delete mode 100644 htslib/cram/._thread_pool.c
delete mode 100644 htslib/cram/._thread_pool.h
delete mode 100644 htslib/cram/._vlen.c
delete mode 100644 htslib/cram/._vlen.h
delete mode 100644 htslib/cram/._zfio.c
delete mode 100644 htslib/cram/._zfio.h
delete mode 100644 htslib/htslib/._bgzf.h
delete mode 100644 htslib/htslib/._cram.h
delete mode 100644 htslib/htslib/._faidx.h
delete mode 100644 htslib/htslib/._hfile.h
delete mode 100644 htslib/htslib/._hts.h
delete mode 100644 htslib/htslib/._hts_defs.h
delete mode 100644 htslib/htslib/._kbitset.h
delete mode 100644 htslib/htslib/._kfunc.h
delete mode 100644 htslib/htslib/._khash.h
delete mode 100644 htslib/htslib/._khash_str2int.h
delete mode 100644 htslib/htslib/._klist.h
delete mode 100644 htslib/htslib/._knetfile.h
delete mode 100644 htslib/htslib/._kseq.h
delete mode 100644 htslib/htslib/._ksort.h
delete mode 100644 htslib/htslib/._kstring.h
delete mode 100644 htslib/htslib/._regidx.h
delete mode 100644 htslib/htslib/._sam.h
delete mode 100644 htslib/htslib/._synced_bcf_reader.h
delete mode 100644 htslib/htslib/._tbx.h
delete mode 100644 htslib/htslib/._vcf.h
delete mode 100644 htslib/htslib/._vcf_sweep.h
delete mode 100644 htslib/htslib/._vcfutils.h
create mode 100755 scripts/count_fixed_catalog_snps.py
create mode 100644 src/constants.cc
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