[med-svn] [tophat] branch master updated (a7b5793 -> 7144f16)
Andreas Tille
tille at debian.org
Wed Dec 6 15:16:17 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository tophat.
from a7b5793 fix tophat compatibility with recent samtools
new c99ecc4 Repack new upstream source without samtools code copy
new b3cee61 New upstream version 2.1.1+dfsg1
new b00fca8 Updated version 2.1.1+dfsg1 from 'upstream/2.1.1+dfsg1'
new 88f1b14 Really remove samtools code copy also from source tarball
new 6d223a3 Versioned Depends: samtools (>= 1.5) [Version since autopkgtest script fails for stretch featuring samtools 1.3!!]
new 698db3f Upload to unstable
new 7144f16 d/watch: enable numbered dfsg-appendices, upload to unstable
The 7 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:
debian/changelog | 7 +-
debian/control | 3 +-
debian/watch | 2 +-
src/intervaltree/__init__.py | 22 -
src/intervaltree/interval.py | 302 --
src/intervaltree/intervaltree.py | 947 -----
src/intervaltree/node.py | 593 ---
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/sortedcontainers/__init__.py | 55 -
src/sortedcontainers/sorteddict.py | 737 ----
src/sortedcontainers/sortedlist.py | 1233 ------
src/sortedcontainers/sortedlistwithkey.py | 1331 -------
src/sortedcontainers/sortedset.py | 294 --
96 files changed, 8 insertions(+), 33703 deletions(-)
delete mode 100755 src/intervaltree/__init__.py
delete mode 100755 src/intervaltree/interval.py
delete mode 100755 src/intervaltree/intervaltree.py
delete mode 100755 src/intervaltree/node.py
delete mode 100644 src/samtools-0.1.18/AUTHORS
delete mode 100644 src/samtools-0.1.18/COPYING
delete mode 100644 src/samtools-0.1.18/ChangeLog
delete mode 100644 src/samtools-0.1.18/INSTALL
delete mode 100644 src/samtools-0.1.18/Makefile
delete mode 100644 src/samtools-0.1.18/Makefile.mingw
delete mode 100644 src/samtools-0.1.18/NEWS
delete mode 100644 src/samtools-0.1.18/bam.c
delete mode 100644 src/samtools-0.1.18/bam.h
delete mode 100644 src/samtools-0.1.18/bam2bcf.c
delete mode 100644 src/samtools-0.1.18/bam2bcf.h
delete mode 100644 src/samtools-0.1.18/bam2bcf_indel.c
delete mode 100644 src/samtools-0.1.18/bam2depth.c
delete mode 100644 src/samtools-0.1.18/bam_aux.c
delete mode 100644 src/samtools-0.1.18/bam_cat.c
delete mode 100644 src/samtools-0.1.18/bam_color.c
delete mode 100644 src/samtools-0.1.18/bam_endian.h
delete mode 100644 src/samtools-0.1.18/bam_import.c
delete mode 100644 src/samtools-0.1.18/bam_index.c
delete mode 100644 src/samtools-0.1.18/bam_lpileup.c
delete mode 100644 src/samtools-0.1.18/bam_mate.c
delete mode 100644 src/samtools-0.1.18/bam_md.c
delete mode 100644 src/samtools-0.1.18/bam_pileup.c
delete mode 100644 src/samtools-0.1.18/bam_plcmd.c
delete mode 100644 src/samtools-0.1.18/bam_reheader.c
delete mode 100644 src/samtools-0.1.18/bam_rmdup.c
delete mode 100644 src/samtools-0.1.18/bam_rmdupse.c
delete mode 100644 src/samtools-0.1.18/bam_sort.c
delete mode 100644 src/samtools-0.1.18/bam_stat.c
delete mode 100644 src/samtools-0.1.18/bam_tview.c
delete mode 100644 src/samtools-0.1.18/bamtk.c
delete mode 100644 src/samtools-0.1.18/bcftools/Makefile
delete mode 100644 src/samtools-0.1.18/bcftools/README
delete mode 100644 src/samtools-0.1.18/bcftools/bcf.c
delete mode 100644 src/samtools-0.1.18/bcftools/bcf.h
delete mode 100644 src/samtools-0.1.18/bcftools/bcf.tex
delete mode 100644 src/samtools-0.1.18/bcftools/bcf2qcall.c
delete mode 100644 src/samtools-0.1.18/bcftools/bcfutils.c
delete mode 100644 src/samtools-0.1.18/bcftools/call1.c
delete mode 100644 src/samtools-0.1.18/bcftools/em.c
delete mode 100644 src/samtools-0.1.18/bcftools/fet.c
delete mode 100644 src/samtools-0.1.18/bcftools/index.c
delete mode 100644 src/samtools-0.1.18/bcftools/kfunc.c
delete mode 100644 src/samtools-0.1.18/bcftools/kmin.c
delete mode 100644 src/samtools-0.1.18/bcftools/kmin.h
delete mode 100644 src/samtools-0.1.18/bcftools/main.c
delete mode 100644 src/samtools-0.1.18/bcftools/mut.c
delete mode 100644 src/samtools-0.1.18/bcftools/prob1.c
delete mode 100644 src/samtools-0.1.18/bcftools/prob1.h
delete mode 100644 src/samtools-0.1.18/bcftools/vcf.c
delete mode 100755 src/samtools-0.1.18/bcftools/vcfutils.pl
delete mode 100644 src/samtools-0.1.18/bedidx.c
delete mode 100644 src/samtools-0.1.18/bgzf.c
delete mode 100644 src/samtools-0.1.18/bgzf.h
delete mode 100644 src/samtools-0.1.18/bgzip.c
delete mode 100644 src/samtools-0.1.18/cut_target.c
delete mode 100644 src/samtools-0.1.18/errmod.c
delete mode 100644 src/samtools-0.1.18/errmod.h
delete mode 100644 src/samtools-0.1.18/faidx.c
delete mode 100644 src/samtools-0.1.18/faidx.h
delete mode 100644 src/samtools-0.1.18/kaln.c
delete mode 100644 src/samtools-0.1.18/kaln.h
delete mode 100644 src/samtools-0.1.18/khash.h
delete mode 100644 src/samtools-0.1.18/klist.h
delete mode 100644 src/samtools-0.1.18/knetfile.c
delete mode 100644 src/samtools-0.1.18/knetfile.h
delete mode 100644 src/samtools-0.1.18/kprobaln.c
delete mode 100644 src/samtools-0.1.18/kprobaln.h
delete mode 100644 src/samtools-0.1.18/kseq.h
delete mode 100644 src/samtools-0.1.18/ksort.h
delete mode 100644 src/samtools-0.1.18/kstring.c
delete mode 100644 src/samtools-0.1.18/kstring.h
delete mode 100644 src/samtools-0.1.18/phase.c
delete mode 100644 src/samtools-0.1.18/razf.c
delete mode 100644 src/samtools-0.1.18/razf.h
delete mode 100644 src/samtools-0.1.18/razip.c
delete mode 100644 src/samtools-0.1.18/sam.c
delete mode 100644 src/samtools-0.1.18/sam.h
delete mode 100644 src/samtools-0.1.18/sam_header.c
delete mode 100644 src/samtools-0.1.18/sam_header.h
delete mode 100644 src/samtools-0.1.18/sam_view.c
delete mode 100644 src/samtools-0.1.18/sample.c
delete mode 100644 src/samtools-0.1.18/sample.h
delete mode 100644 src/samtools-0.1.18/samtools.1
delete mode 100755 src/sortedcontainers/__init__.py
delete mode 100755 src/sortedcontainers/sorteddict.py
delete mode 100755 src/sortedcontainers/sortedlist.py
delete mode 100755 src/sortedcontainers/sortedlistwithkey.py
delete mode 100755 src/sortedcontainers/sortedset.py
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