[med-svn] [stacks] branch debian/jessie-backports updated (e64afba -> be5bd71)
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 change to branch debian/jessie-backports
in repository stacks.
from e64afba Rebuild for jessie-backports
adds 83ef6c3 Imported Upstream version 1.38
adds bb0755c Merge tag 'upstream/1.38'
adds 5e7e762 New upstream version
adds c78f272 Enable PHP migration
adds f61a805 Better hardening and upload to unstable
adds 709db0d Imported Upstream version 1.40
adds 8a0b5fe New upstream version
adds f7c6a7f cme fix dpkg-control
adds e44c3dd Build-Depends: samtools to ensure that package builds only on those architectures where samtools is available
adds c0ff32a Add Python depencency since new tool in Python was included by upstream
adds 7773661 Imported Upstream version 1.40
adds df2c72a Imported Upstream version 1.42
adds 7100acd Merge tag 'upstream/1.42'
adds 3cc7810 New upstream version, does not build with -pie hardening option so this is removed
adds 750b9f1 Fix script executable paths to debian install dir
adds 1d2ea27 New upstream version 1.44
adds d1ee70b Merge tag 'upstream/1.44'
adds 91b80e2 New upstream version
adds b7af9c0 stacks-web Depends: default-mysql-server | mysql-server
adds 8d9bc5d d/watch: version=4
adds 1a9ee0c debhelper 10
adds e1f5b16 stacks-web: Depends s/ | mysql-server/ | virtual-mysql-server/
adds 05da8e5 Upload to unstable
new dd4ce9e Merge branch 'master' into debian/jessie-backports
new be5bd71 Rebuild for jessie-backports
The 2 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 | 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 | 51 +
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, 79454 insertions(+), 24737 deletions(-)
create mode 100644 debian/patches/script-exe-paths
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 100755 scripts/integrate_alignments.py
create mode 100644 src/GappedAln.h
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/aln_utils.cc
create mode 100644 src/aln_utils.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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