[med-svn] [tophat] branch master updated (72fcdd6 -> e569c47)
Andreas Tille
tille at debian.org
Sat Oct 4 19:33:18 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository tophat.
from 72fcdd6 fix "empty-short-license-in-dep5-copyright" lintian warnings
new 9a58423 Imported Upstream version 2.0.13
new 0a95530 Merge tag 'upstream/2.0.13'
new 5e25c97 New upstream version
new b04eb82 Imported Upstream version 2.0.13+dfsg
new e569c47 Merge tag 'upstream/2.0.13+dfsg'
The 5 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:
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 +-
debian/changelog | 6 +
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 +-
115 files changed, 30200 insertions(+), 2101 deletions(-)
delete mode 100644 ax_bam.m4
rename build-aux/config.guess => config.guess (100%)
rename build-aux/config.sub => config.sub (100%)
rename build-aux/depcomp => depcomp (100%)
rename build-aux/install-sh => install-sh (100%)
rename build-aux/missing => missing (100%)
create mode 100644 src/samtools-0.1.18/AUTHORS
create mode 100644 src/samtools-0.1.18/COPYING
create mode 100644 src/samtools-0.1.18/ChangeLog
create mode 100644 src/samtools-0.1.18/INSTALL
create mode 100644 src/samtools-0.1.18/Makefile
create mode 100644 src/samtools-0.1.18/Makefile.mingw
create mode 100644 src/samtools-0.1.18/NEWS
create mode 100644 src/samtools-0.1.18/bam.c
create mode 100644 src/samtools-0.1.18/bam.h
create mode 100644 src/samtools-0.1.18/bam2bcf.c
create mode 100644 src/samtools-0.1.18/bam2bcf.h
create mode 100644 src/samtools-0.1.18/bam2bcf_indel.c
create mode 100644 src/samtools-0.1.18/bam2depth.c
create mode 100644 src/samtools-0.1.18/bam_aux.c
create mode 100644 src/samtools-0.1.18/bam_cat.c
create mode 100644 src/samtools-0.1.18/bam_color.c
create mode 100644 src/samtools-0.1.18/bam_endian.h
create mode 100644 src/samtools-0.1.18/bam_import.c
create mode 100644 src/samtools-0.1.18/bam_index.c
create mode 100644 src/samtools-0.1.18/bam_lpileup.c
create mode 100644 src/samtools-0.1.18/bam_mate.c
create mode 100644 src/samtools-0.1.18/bam_md.c
create mode 100644 src/samtools-0.1.18/bam_pileup.c
create mode 100644 src/samtools-0.1.18/bam_plcmd.c
create mode 100644 src/samtools-0.1.18/bam_reheader.c
create mode 100644 src/samtools-0.1.18/bam_rmdup.c
create mode 100644 src/samtools-0.1.18/bam_rmdupse.c
create mode 100644 src/samtools-0.1.18/bam_sort.c
create mode 100644 src/samtools-0.1.18/bam_stat.c
create mode 100644 src/samtools-0.1.18/bam_tview.c
create mode 100644 src/samtools-0.1.18/bamtk.c
create mode 100644 src/samtools-0.1.18/bcftools/Makefile
create mode 100644 src/samtools-0.1.18/bcftools/README
create mode 100644 src/samtools-0.1.18/bcftools/bcf.c
create mode 100644 src/samtools-0.1.18/bcftools/bcf.h
create mode 100644 src/samtools-0.1.18/bcftools/bcf.tex
create mode 100644 src/samtools-0.1.18/bcftools/bcf2qcall.c
create mode 100644 src/samtools-0.1.18/bcftools/bcfutils.c
create mode 100644 src/samtools-0.1.18/bcftools/call1.c
create mode 100644 src/samtools-0.1.18/bcftools/em.c
create mode 100644 src/samtools-0.1.18/bcftools/fet.c
create mode 100644 src/samtools-0.1.18/bcftools/index.c
create mode 100644 src/samtools-0.1.18/bcftools/kfunc.c
create mode 100644 src/samtools-0.1.18/bcftools/kmin.c
create mode 100644 src/samtools-0.1.18/bcftools/kmin.h
create mode 100644 src/samtools-0.1.18/bcftools/main.c
create mode 100644 src/samtools-0.1.18/bcftools/mut.c
create mode 100644 src/samtools-0.1.18/bcftools/prob1.c
create mode 100644 src/samtools-0.1.18/bcftools/prob1.h
create mode 100644 src/samtools-0.1.18/bcftools/vcf.c
create mode 100755 src/samtools-0.1.18/bcftools/vcfutils.pl
create mode 100644 src/samtools-0.1.18/bedidx.c
create mode 100644 src/samtools-0.1.18/bgzf.c
create mode 100644 src/samtools-0.1.18/bgzf.h
create mode 100644 src/samtools-0.1.18/bgzip.c
create mode 100644 src/samtools-0.1.18/cut_target.c
create mode 100644 src/samtools-0.1.18/errmod.c
create mode 100644 src/samtools-0.1.18/errmod.h
create mode 100644 src/samtools-0.1.18/faidx.c
create mode 100644 src/samtools-0.1.18/faidx.h
create mode 100644 src/samtools-0.1.18/kaln.c
create mode 100644 src/samtools-0.1.18/kaln.h
create mode 100644 src/samtools-0.1.18/khash.h
create mode 100644 src/samtools-0.1.18/klist.h
create mode 100644 src/samtools-0.1.18/knetfile.c
create mode 100644 src/samtools-0.1.18/knetfile.h
create mode 100644 src/samtools-0.1.18/kprobaln.c
create mode 100644 src/samtools-0.1.18/kprobaln.h
create mode 100644 src/samtools-0.1.18/kseq.h
create mode 100644 src/samtools-0.1.18/ksort.h
create mode 100644 src/samtools-0.1.18/kstring.c
create mode 100644 src/samtools-0.1.18/kstring.h
create mode 100644 src/samtools-0.1.18/phase.c
create mode 100644 src/samtools-0.1.18/razf.c
create mode 100644 src/samtools-0.1.18/razf.h
create mode 100644 src/samtools-0.1.18/razip.c
create mode 100644 src/samtools-0.1.18/sam.c
create mode 100644 src/samtools-0.1.18/sam.h
create mode 100644 src/samtools-0.1.18/sam_header.c
create mode 100644 src/samtools-0.1.18/sam_header.h
create mode 100644 src/samtools-0.1.18/sam_view.c
create mode 100644 src/samtools-0.1.18/sample.c
create mode 100644 src/samtools-0.1.18/sample.h
create mode 100644 src/samtools-0.1.18/samtools.1
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