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commit 7100acd0cd1ed14a73dbd64236603a8d0164055a Merge: c0ff32a df2c72a Author: Andreas Tille <[email protected]> Date: Sat Aug 13 10:49:24 2016 +0200 Merge tag 'upstream/1.42' Upstream version 1.42 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/stacks.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
