[med-svn] [stacks] 01/02: Merge branch 'master' into debian/jessie-backports
Andreas Tille
tille at debian.org
Fri Jun 9 20:05:04 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch debian/jessie-backports
in repository stacks.
commit dd4ce9ec2b466c00e8cfff5b26cb6a7fb8051a25
Merge: e64afba 05da8e5
Author: Andreas Tille <tille at debian.org>
Date: Fri Jun 9 21:25:27 2017 +0200
Merge branch 'master' into debian/jessie-backports
ChangeLog | 83 +
Makefile.am | 39 +-
Makefile.in | 740 +-
README | 33 +-
acinclude.m4 | 583 +-
aclocal.m4 | 65 +-
config/compile | 2 +-
config/depcomp | 2 +-
config/install-sh | 366 +-
config/missing | 2 +-
config/test-driver | 15 +-
configure | 961 +-
configure.ac | 27 +-
debian/changelog | 45 +
debian/compat | 2 +-
debian/control | 13 +-
debian/patches/script-exe-paths | 38 +
debian/patches/series | 1 +
debian/rules | 5 +-
debian/watch | 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 ++
php/CatalogClass.php | 8 +-
php/catalog.php | 5 +-
php/export_batch.php | 6 +
scripts/denovo_map.pl | 1015 +-
scripts/integrate_alignments.py | 426 +
scripts/load_sequences.pl | 2 +-
scripts/ref_map.pl | 969 +-
sql/stacks.sql | 1 +
src/BamI.h | 472 +-
src/BamUnalignedI.h | 112 +-
src/BowtieI.h | 23 +-
src/BustardI.h | 38 +-
src/DNANSeq.cc | 133 +-
src/DNANSeq.h | 92 +-
src/DNASeq.cc | 328 +-
src/DNASeq.h | 24 +-
src/FastaI.h | 40 +-
src/FastqI.h | 24 +-
src/GappedAln.h | 594 +
src/MetaPopInfo.cc | 347 +
src/MetaPopInfo.h | 111 +
src/PopMap.h | 477 +-
src/PopSum.h | 1273 ++-
src/SamI.h | 347 +-
src/Tsv.h | 20 +-
src/Vcf.cc | 506 +
src/Vcf.h | 467 +
src/aln_utils.cc | 471 +
src/aln_utils.h | 47 +
src/bootstrap.h | 446 +-
src/catalog_utils.cc | 464 +-
src/catalog_utils.h | 44 +
src/clean.cc | 712 +-
src/clean.h | 488 +-
src/clone_filter.cc | 1396 +--
src/clone_filter.h | 16 +-
src/cmb.cc | 20 +-
src/cmb.h | 4 +-
src/constants.h | 16 +-
src/cstacks.cc | 1934 ++--
src/cstacks.h | 7 +-
src/estacks.cc | 576 +-
src/estacks.h | 2 +-
src/export_formats.cc | 3333 ++++++
src/export_formats.h | 70 +
src/file_io.cc | 1494 +--
src/file_io.h | 16 +-
...ype_dictionaries.h => genotype_dictionaries.cc} | 224 +-
src/genotype_dictionaries.h | 558 +-
src/genotypes.cc | 2556 +++--
src/genotypes.h | 2 +-
src/gzFasta.h | 86 +-
src/gzFastq.h | 62 +-
src/hstacks.cc | 372 +-
src/input.cc | 219 +-
src/input.h | 31 +-
src/kmer_filter.cc | 2134 ++--
src/kmer_filter.h | 2 +-
src/kmers.cc | 293 +-
src/kmers.h | 25 +-
src/locus.cc | 110 +-
src/locus.h | 59 +-
src/log_utils.cc | 4 +-
src/models.cc | 558 +-
src/mst.cc | 26 +-
src/mst.h | 4 +-
src/mstack.cc | 157 +-
src/mstack.h | 18 +-
src/ordered.h | 334 +-
src/phasedstacks.cc | 2010 ++--
src/phasedstacks.h | 124 +-
src/populations.cc | 10984 +++++++------------
src/populations.h | 131 +-
src/process_radtags.cc | 1511 +--
src/process_radtags.h | 30 +-
src/process_shortreads.cc | 1406 +--
src/process_shortreads.h | 30 +-
src/pstacks.cc | 1040 +-
src/pstacks.h | 7 +-
src/{renz.h => renz.cc} | 119 +-
src/renz.h | 219 +-
src/rxstacks.cc | 2229 ++--
src/rxstacks.h | 11 +-
src/smoothing.h | 171 +-
src/smoothing_utils.h | 42 +-
src/sql_utilities.cc | 299 +
src/sql_utilities.h | 680 +-
src/sstacks.cc | 1368 ++-
src/sstacks.h | 32 +-
src/stacks.cc | 34 +-
src/stacks.h | 232 +-
src/ustacks.cc | 2995 ++---
src/ustacks.h | 46 +-
src/utils.cc | 104 +-
src/utils.h | 6 +-
src/write.cc | 268 +-
src/write.h | 2 +-
303 files changed, 79448 insertions(+), 24737 deletions(-)
diff --cc debian/changelog
index c8f8a53,76e68b5..b2e7a30
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,48 +1,54 @@@
+ stacks (1.44-2) unstable; urgency=medium
+
+ * d/watch: version=4
+ * debhelper 10
+ * stacks-web: Depends s/ | mysql-server/ | virtual-mysql-server/
+ Closes: #848464
+
+ -- Andreas Tille <tille at debian.org> Sat, 17 Dec 2016 17:34:44 +0100
+
+ stacks (1.44-1) unstable; urgency=medium
+
+ [ Kevin Murray ]
+ * Fix script executable paths to reflect debian install directory
+
+ [ Andreas Tille ]
+ * New upstream version
+ * stacks-web Depends: default-mysql-server | mysql-server
+
+ -- Andreas Tille <tille at debian.org> Sat, 22 Oct 2016 21:04:24 +0200
+
+ stacks (1.42-1) unstable; urgency=medium
+
+ * New upstream version
+ * hardening -pie
+
+ -- Andreas Tille <tille at debian.org> Sat, 13 Aug 2016 10:49:42 +0200
+
+ stacks (1.40-1) unstable; urgency=medium
+
+ * New upstream version
+ * cme fix dpkg-control
+ * Build-Depends: samtools to ensure that package builds only on those
+ architectures where samtools is available
+
+ -- Andreas Tille <tille at debian.org> Thu, 19 May 2016 12:55:47 +0200
+
+ stacks (1.38-1) unstable; urgency=medium
+
+ * New upstream version
+ * debian/control: s/php5/php/
+ Closes: #821664
+ * Better hardening
+
+ -- Andreas Tille <tille at debian.org> Tue, 19 Apr 2016 10:45:21 +0200
+
+stacks (1.37-1~bpo8+1) jessie-backports; urgency=medium
+
+ * Rebuild for jessie-backports.
+
+ -- Andreas Tille <tille at debian.org> Thu, 07 Apr 2016 08:43:15 +0200
+
stacks (1.37-1) unstable; urgency=medium
* New upstream version
--
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