[med-svn] [tophat] 02/05: Merge tag 'upstream/2.0.13'
Andreas Tille
tille at debian.org
Sat Oct 4 19:33:18 UTC 2014
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tille pushed a commit to branch master
in repository tophat.
commit 0a95530417d3282c33150f442ca638978f5f0cfe
Merge: 72fcdd6 9a58423
Author: Andreas Tille <tille at debian.org>
Date: Sat Oct 4 21:29:55 2014 +0200
Merge tag 'upstream/2.0.13'
Upstream version 2.0.13
AUTHORS | 33 +-
COPYING | 1 -
Makefile.am | 1 -
Makefile.in | 14 +-
README | 25 +-
ax_bam.m4 | 203 -
ax_boost_thread.m4 | 246 +-
build-aux/config.guess => config.guess | 0
config.h.in | 6 +-
build-aux/config.sub => config.sub | 0
configure | 2943 ++++++++-------
configure.ac | 45 +-
build-aux/depcomp => depcomp | 0
build-aux/install-sh => install-sh | 0
build-aux/missing => missing | 0
src/GBase.cpp | 49 +-
src/GBase.h | 2 +-
src/Makefile.am | 126 +-
src/Makefile.in | 209 +-
src/align_status.h | 2 +-
src/bam2fastx.cpp | 4 +-
src/bed_to_juncs | 7 +-
src/bwt_map.h | 10 +-
src/common.cpp | 2 +-
src/common.h | 4 +-
src/map2gtf.h | 4 +-
src/samtools-0.1.18/AUTHORS | 20 +
src/samtools-0.1.18/COPYING | 21 +
src/samtools-0.1.18/ChangeLog | 5948 ++++++++++++++++++++++++++++++
src/samtools-0.1.18/INSTALL | 30 +
src/samtools-0.1.18/Makefile | 93 +
src/samtools-0.1.18/Makefile.mingw | 63 +
src/samtools-0.1.18/NEWS | 806 ++++
src/samtools-0.1.18/bam.c | 362 ++
src/samtools-0.1.18/bam.h | 763 ++++
src/samtools-0.1.18/bam2bcf.c | 351 ++
src/samtools-0.1.18/bam2bcf.h | 57 +
src/samtools-0.1.18/bam2bcf_indel.c | 475 +++
src/samtools-0.1.18/bam2depth.c | 112 +
src/samtools-0.1.18/bam_aux.c | 213 ++
src/samtools-0.1.18/bam_cat.c | 184 +
src/samtools-0.1.18/bam_color.c | 127 +
src/samtools-0.1.18/bam_endian.h | 42 +
src/samtools-0.1.18/bam_import.c | 485 +++
src/samtools-0.1.18/bam_index.c | 719 ++++
src/samtools-0.1.18/bam_lpileup.c | 198 +
src/samtools-0.1.18/bam_mate.c | 70 +
src/samtools-0.1.18/bam_md.c | 384 ++
src/samtools-0.1.18/bam_pileup.c | 437 +++
src/samtools-0.1.18/bam_plcmd.c | 546 +++
src/samtools-0.1.18/bam_reheader.c | 61 +
src/samtools-0.1.18/bam_rmdup.c | 206 ++
src/samtools-0.1.18/bam_rmdupse.c | 159 +
src/samtools-0.1.18/bam_sort.c | 438 +++
src/samtools-0.1.18/bam_stat.c | 77 +
src/samtools-0.1.18/bam_tview.c | 440 +++
src/samtools-0.1.18/bamtk.c | 109 +
src/samtools-0.1.18/bcftools/Makefile | 51 +
src/samtools-0.1.18/bcftools/README | 36 +
src/samtools-0.1.18/bcftools/bcf.c | 328 ++
src/samtools-0.1.18/bcftools/bcf.h | 190 +
src/samtools-0.1.18/bcftools/bcf.tex | 77 +
src/samtools-0.1.18/bcftools/bcf2qcall.c | 91 +
src/samtools-0.1.18/bcftools/bcfutils.c | 390 ++
src/samtools-0.1.18/bcftools/call1.c | 586 +++
src/samtools-0.1.18/bcftools/em.c | 310 ++
src/samtools-0.1.18/bcftools/fet.c | 112 +
src/samtools-0.1.18/bcftools/index.c | 335 ++
src/samtools-0.1.18/bcftools/kfunc.c | 162 +
src/samtools-0.1.18/bcftools/kmin.c | 209 ++
src/samtools-0.1.18/bcftools/kmin.h | 46 +
src/samtools-0.1.18/bcftools/main.c | 190 +
src/samtools-0.1.18/bcftools/mut.c | 127 +
src/samtools-0.1.18/bcftools/prob1.c | 554 +++
src/samtools-0.1.18/bcftools/prob1.h | 42 +
src/samtools-0.1.18/bcftools/vcf.c | 244 ++
src/samtools-0.1.18/bcftools/vcfutils.pl | 567 +++
src/samtools-0.1.18/bedidx.c | 162 +
src/samtools-0.1.18/bgzf.c | 714 ++++
src/samtools-0.1.18/bgzf.h | 157 +
src/samtools-0.1.18/bgzip.c | 206 ++
src/samtools-0.1.18/cut_target.c | 193 +
src/samtools-0.1.18/errmod.c | 130 +
src/samtools-0.1.18/errmod.h | 24 +
src/samtools-0.1.18/faidx.c | 432 +++
src/samtools-0.1.18/faidx.h | 103 +
src/samtools-0.1.18/kaln.c | 486 +++
src/samtools-0.1.18/kaln.h | 67 +
src/samtools-0.1.18/khash.h | 528 +++
src/samtools-0.1.18/klist.h | 96 +
src/samtools-0.1.18/knetfile.c | 632 ++++
src/samtools-0.1.18/knetfile.h | 75 +
src/samtools-0.1.18/kprobaln.c | 278 ++
src/samtools-0.1.18/kprobaln.h | 49 +
src/samtools-0.1.18/kseq.h | 224 ++
src/samtools-0.1.18/ksort.h | 281 ++
src/samtools-0.1.18/kstring.c | 212 ++
src/samtools-0.1.18/kstring.h | 117 +
src/samtools-0.1.18/phase.c | 687 ++++
src/samtools-0.1.18/razf.c | 853 +++++
src/samtools-0.1.18/razf.h | 134 +
src/samtools-0.1.18/razip.c | 141 +
src/samtools-0.1.18/sam.c | 179 +
src/samtools-0.1.18/sam.h | 98 +
src/samtools-0.1.18/sam_header.c | 736 ++++
src/samtools-0.1.18/sam_header.h | 24 +
src/samtools-0.1.18/sam_view.c | 406 ++
src/samtools-0.1.18/sample.c | 107 +
src/samtools-0.1.18/sample.h | 17 +
src/samtools-0.1.18/samtools.1 | 994 +++++
src/segment_juncs.cpp | 143 +-
src/tophat-fusion-post | 2 +-
src/tophat.py | 21 +-
src/tophat_reports.cpp | 8 +-
114 files changed, 30194 insertions(+), 2101 deletions(-)
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