[med-svn] [tophat] branch upstream updated (5e1ff73 -> b3cee61)
Andreas Tille
tille at debian.org
Wed Dec 6 15:16:21 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository tophat.
from 5e1ff73 Imported Upstream version 2.1.1+dfsg
new b3cee61 New upstream version 2.1.1+dfsg1
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:
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 --
93 files changed, 33699 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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