[med-svn] [python-pysam] 02/04: Merge tag 'upstream/0.11.2.2+ds'
Afif Elghraoui
afif at moszumanska.debian.org
Tue Jul 4 04:25:07 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository python-pysam.
commit 21a9d046a132019cfcd185ba933cddd88fd2d489
Merge: b8fd88f 1520aab
Author: Afif Elghraoui <afif at debian.org>
Date: Sun Jul 2 03:51:28 2017 -0400
Merge tag 'upstream/0.11.2.2+ds'
Upstream version 0.11.2.2+ds
.gitignore | 14 +-
MANIFEST.in | 7 +-
bcftools/HMM.c | 141 +-
bcftools/HMM.c.pysam.c | 141 +-
bcftools/HMM.h | 26 +-
{samtools => bcftools}/bam2bcf.c | 54 +-
{samtools => bcftools}/bam2bcf.c.pysam.c | 54 +-
{samtools => bcftools}/bam2bcf.h | 7 +-
{samtools => bcftools}/bam2bcf_indel.c | 141 +-
{samtools => bcftools}/bam2bcf_indel.c.pysam.c | 141 +-
bcftools/bam_sample.c | 393 ++
bcftools/bam_sample.c.pysam.c | 395 ++
samtools/errmod.h => bcftools/bam_sample.h | 41 +-
bcftools/bcftools.h | 1 +
bcftools/bin.c | 104 +
bcftools/bin.c.pysam.c | 106 +
bcftools/bin.h | 65 +
bcftools/call.h | 3 +-
bcftools/ccall.c | 10 +-
bcftools/ccall.c.pysam.c | 10 +-
bcftools/consensus.c | 56 +-
bcftools/consensus.c.pysam.c | 56 +-
bcftools/convert.c | 490 ++-
bcftools/convert.c.pysam.c | 490 ++-
bcftools/csq.c | 3824 +++++++++++++++++++
bcftools/csq.c.pysam.c | 3826 ++++++++++++++++++++
bcftools/filter.c | 357 +-
bcftools/filter.c.pysam.c | 357 +-
bcftools/hclust.c | 400 ++
bcftools/hclust.c.pysam.c | 402 ++
bcftools/hclust.h | 77 +
bcftools/kheap.h | 171 +
bcftools/main.c | 10 +
bcftools/main.c.pysam.c | 10 +
bcftools/mcall.c | 228 +-
bcftools/mcall.c.pysam.c | 228 +-
bcftools/mpileup.c | 1110 ++++++
bcftools/mpileup.c.pysam.c | 1112 ++++++
bcftools/mw.h | 1944 ++++++++++
bcftools/ploidy.c | 22 +-
bcftools/ploidy.c.pysam.c | 22 +-
bcftools/ploidy.h | 2 +-
bcftools/prob1.c | 12 +-
bcftools/prob1.c.pysam.c | 12 +-
bcftools/prob1.h | 2 +-
bcftools/regidx.c | 598 +++
bcftools/regidx.c.pysam.c | 600 +++
bcftools/regidx.h | 191 +
bcftools/smpl_ilist.c | 106 +
bcftools/smpl_ilist.c.pysam.c | 108 +
bcftools/smpl_ilist.h | 47 +
bcftools/tabix.c | 30 +-
bcftools/tabix.c.pysam.c | 30 +-
bcftools/tsv2vcf.c | 1 +
bcftools/tsv2vcf.c.pysam.c | 1 +
bcftools/vcfannotate.c | 744 ++--
bcftools/vcfannotate.c.pysam.c | 744 ++--
bcftools/vcfcall.c | 44 +-
bcftools/vcfcall.c.pysam.c | 44 +-
bcftools/vcfcnv.c | 46 +-
bcftools/vcfcnv.c.pysam.c | 46 +-
bcftools/vcfconcat.c | 164 +-
bcftools/vcfconcat.c.pysam.c | 164 +-
bcftools/vcfconvert.c | 120 +-
bcftools/vcfconvert.c.pysam.c | 120 +-
bcftools/vcffilter.c | 3 +-
bcftools/vcffilter.c.pysam.c | 3 +-
bcftools/vcfgtcheck.c | 298 +-
bcftools/vcfgtcheck.c.pysam.c | 298 +-
bcftools/vcfindex.c | 115 +-
bcftools/vcfindex.c.pysam.c | 115 +-
bcftools/vcfmerge.c | 1075 ++++--
bcftools/vcfmerge.c.pysam.c | 1075 ++++--
bcftools/vcfnorm.c | 82 +-
bcftools/vcfnorm.c.pysam.c | 82 +-
bcftools/vcfplugin.c | 56 +-
bcftools/vcfplugin.c.pysam.c | 56 +-
bcftools/vcfroh.c | 961 +++--
bcftools/vcfroh.c.pysam.c | 961 +++--
bcftools/vcfstats.c | 429 ++-
bcftools/vcfstats.c.pysam.c | 429 ++-
bcftools/vcfview.c | 50 +-
bcftools/vcfview.c.pysam.c | 50 +-
bcftools/version.h | 2 +-
buildwheels.sh | 2 +-
doc/api.rst | 4 +-
doc/release.rst | 75 +
doc/usage.rst | 19 +-
import.py | 29 +-
pysam/__init__.py | 2 +
pysam/cbcftools_util.h | 6 +
pysam/csamtools_util.h | 6 +
pysam/htslib_util.h | 20 -
pysam/libcalignedsegment.pxd | 6 -
pysam/libcalignedsegment.pyx | 288 +-
pysam/libcalignmentfile.pyx | 344 +-
pysam/libcbcf.pxd | 21 +-
pysam/libcbcf.pyx | 848 ++++-
pysam/libcbcftools.pxd | 3 +
pysam/libcbcftools.pyx | 2 +
pysam/libcbgzf.pyx | 53 +-
pysam/libcfaidx.pyx | 31 +-
pysam/libchtslib.pxd | 679 +++-
pysam/libchtslib.pyx | 285 +-
pysam/libcsamtools.pxd | 3 +
pysam/libcsamtools.pyx | 2 +
pysam/libctabix.pxd | 4 +
pysam/libctabix.pyx | 42 +-
pysam/libctabixproxies.pxd | 14 +-
pysam/libctabixproxies.pyx | 506 ++-
pysam/libcutils.pxd | 4 +-
pysam/libcutils.pyx | 30 +-
pysam/pysam_util.c | 6 +-
pysam/pysam_util.h | 4 +
pysam/samfile_util.c | 172 -
pysam/samfile_util.h | 3 -
pysam/tabix_util.c | 1 +
pysam/utils.py | 13 +-
pysam/version.py | 11 +-
samtools/bam.h | 2 +-
samtools/bam2bcf.c | 2 +-
samtools/bam2bcf.c.pysam.c | 2 +-
samtools/bam2bcf.h | 2 +-
samtools/bam2bcf_indel.c | 26 +-
samtools/bam2bcf_indel.c.pysam.c | 26 +-
samtools/bam2depth.c | 30 +-
samtools/bam2depth.c.pysam.c | 30 +-
samtools/bam_addrprg.c | 86 +-
samtools/bam_addrprg.c.pysam.c | 86 +-
samtools/bam_cat.c | 60 +-
samtools/bam_cat.c.pysam.c | 60 +-
samtools/bam_index.c | 52 +-
samtools/bam_index.c.pysam.c | 52 +-
samtools/bam_mate.c | 71 +-
samtools/bam_mate.c.pysam.c | 71 +-
samtools/bam_md.c | 202 +-
samtools/bam_md.c.pysam.c | 204 +-
samtools/bam_plcmd.c | 122 +-
samtools/bam_plcmd.c.pysam.c | 122 +-
samtools/bam_quickcheck.c | 52 +-
samtools/bam_quickcheck.c.pysam.c | 52 +-
samtools/bam_reheader.c | 4 +-
samtools/bam_reheader.c.pysam.c | 14 +-
samtools/bam_rmdup.c | 4 +-
samtools/bam_rmdup.c.pysam.c | 4 +-
samtools/bam_sort.c | 178 +-
samtools/bam_sort.c.pysam.c | 178 +-
samtools/bam_split.c | 99 +-
samtools/bam_split.c.pysam.c | 99 +-
samtools/bam_stat.c | 28 +-
samtools/bam_stat.c.pysam.c | 38 +-
samtools/bam_tview.c | 441 ---
samtools/bam_tview.c.pysam.c | 443 ---
samtools/bam_tview.h | 105 -
samtools/bam_tview_curses.c | 352 --
samtools/bam_tview_curses.c.pysam.c | 354 --
samtools/bam_tview_html.c | 377 --
samtools/bam_tview_html.c.pysam.c | 379 --
samtools/bamshuf.c | 22 +-
samtools/bamshuf.c.pysam.c | 22 +-
samtools/bamtk.c | 35 +-
samtools/bamtk.c.pysam.c | 39 +-
samtools/bedcov.c | 8 +-
samtools/bedcov.c.pysam.c | 8 +-
samtools/cut_target.c | 19 +-
samtools/cut_target.c.pysam.c | 19 +-
samtools/errmod.c | 194 -
samtools/errmod.c.pysam.c | 196 -
samtools/faidx.c | 74 +-
samtools/faidx.c.pysam.c | 74 +-
samtools/kprobaln.c | 282 --
samtools/kprobaln.c.pysam.c | 284 --
samtools/kprobaln.h | 49 -
samtools/misc/ace2sam.c | 5 +-
samtools/misc/ace2sam.c.pysam.c | 5 +-
samtools/padding.c | 4 +-
samtools/padding.c.pysam.c | 4 +-
samtools/phase.c | 6 +-
samtools/phase.c.pysam.c | 6 +-
samtools/sam.h | 2 +-
samtools/sam_opts.c | 8 +-
samtools/sam_opts.c.pysam.c | 8 +-
samtools/sam_opts.h | 7 +-
samtools/{test/test.c => sam_utils.c} | 51 +-
.../{test/test.c.pysam.c => sam_utils.c.pysam.c} | 51 +-
samtools/sam_view.c | 498 ++-
samtools/sam_view.c.pysam.c | 500 ++-
samtools/stats.c | 20 +-
samtools/stats.c.pysam.c | 29 +-
samtools/test/split/test_filter_header_rg.c | 15 +-
.../test/split/test_filter_header_rg.c.pysam.c | 15 +-
samtools/test/test.c | 8 +-
samtools/test/test.c.pysam.c | 8 +-
samtools/version.h | 2 +-
setup.py | 69 +-
tests/AlignedSegment_test.py | 93 +-
tests/AlignmentFile_test.py | 143 +-
tests/SamFile_test.py | 1990 ----------
tests/StreamFiledescriptors_test.py | 71 +-
tests/TestUtils.py | 32 +-
tests/VariantFile_test.py | 5 +-
tests/faidx_test.py | 14 +-
tests/samtools_test.py | 47 +-
tests/tabix_data/example.gff2.gz | Bin 0 -> 238 bytes
tests/tabix_data/example.gff2.gz.tbi | Bin 0 -> 107 bytes
tests/tabix_data/example.gff3.gz | Bin 0 -> 3067 bytes
tests/tabix_data/example.gff3.gz.tbi | Bin 0 -> 1457 bytes
tests/tabix_test.py | 262 +-
tests/tabixproxies_test.py | 318 ++
209 files changed, 28682 insertions(+), 12148 deletions(-)
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