[med-svn] [python-pysam] branch upstream updated (dadf905 -> 1520aab)
Afif Elghraoui
afif at moszumanska.debian.org
Tue Jul 4 04:25:10 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository python-pysam.
from dadf905 Imported Upstream version 0.10.0+ds
new 1520aab Imported Upstream version 0.11.2.2+ds
The 1 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:
.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/{gvcf.h => bin.h} | 48 +-
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/{samtools.h => sam_utils.c} | 57 +-
samtools/{samtools.h => sam_utils.c.pysam.c} | 59 +-
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, 28677 insertions(+), 12150 deletions(-)
copy {samtools => bcftools}/bam2bcf.c (96%)
copy {samtools => bcftools}/bam2bcf.c.pysam.c (96%)
copy {samtools => bcftools}/bam2bcf.h (96%)
copy {samtools => bcftools}/bam2bcf_indel.c (83%)
copy {samtools => bcftools}/bam2bcf_indel.c.pysam.c (83%)
create mode 100644 bcftools/bam_sample.c
create mode 100644 bcftools/bam_sample.c.pysam.c
rename samtools/errmod.h => bcftools/bam_sample.h (53%)
create mode 100644 bcftools/bin.c
create mode 100644 bcftools/bin.c.pysam.c
copy bcftools/{gvcf.h => bin.h} (52%)
create mode 100644 bcftools/csq.c
create mode 100644 bcftools/csq.c.pysam.c
create mode 100644 bcftools/hclust.c
create mode 100644 bcftools/hclust.c.pysam.c
create mode 100644 bcftools/hclust.h
create mode 100644 bcftools/kheap.h
create mode 100644 bcftools/mpileup.c
create mode 100644 bcftools/mpileup.c.pysam.c
create mode 100644 bcftools/mw.h
create mode 100644 bcftools/regidx.c
create mode 100644 bcftools/regidx.c.pysam.c
create mode 100644 bcftools/regidx.h
create mode 100644 bcftools/smpl_ilist.c
create mode 100644 bcftools/smpl_ilist.c.pysam.c
create mode 100644 bcftools/smpl_ilist.h
create mode 100644 pysam/cbcftools_util.h
create mode 100644 pysam/csamtools_util.h
create mode 100644 pysam/libcbcftools.pxd
create mode 100644 pysam/libcbcftools.pyx
create mode 100644 pysam/libcsamtools.pxd
create mode 100644 pysam/libcsamtools.pyx
delete mode 100644 samtools/bam_tview.c
delete mode 100644 samtools/bam_tview.c.pysam.c
delete mode 100644 samtools/bam_tview.h
delete mode 100644 samtools/bam_tview_curses.c
delete mode 100644 samtools/bam_tview_curses.c.pysam.c
delete mode 100644 samtools/bam_tview_html.c
delete mode 100644 samtools/bam_tview_html.c.pysam.c
delete mode 100644 samtools/errmod.c
delete mode 100644 samtools/errmod.c.pysam.c
delete mode 100644 samtools/kprobaln.c
delete mode 100644 samtools/kprobaln.c.pysam.c
delete mode 100644 samtools/kprobaln.h
copy samtools/{samtools.h => sam_utils.c} (54%)
copy samtools/{samtools.h => sam_utils.c.pysam.c} (53%)
delete mode 100644 tests/SamFile_test.py
create mode 100644 tests/tabix_data/example.gff2.gz
create mode 100644 tests/tabix_data/example.gff2.gz.tbi
create mode 100644 tests/tabix_data/example.gff3.gz
create mode 100644 tests/tabix_data/example.gff3.gz.tbi
create mode 100644 tests/tabixproxies_test.py
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