[med-svn] [tophat] 03/07: Updated version 2.1.1+dfsg1 from 'upstream/2.1.1+dfsg1'
Andreas Tille
tille at debian.org
Wed Dec 6 15:16:19 UTC 2017
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tille pushed a commit to branch master
in repository tophat.
commit b00fca821b5a10b70c213779ab3eeb786a3a88ed
Merge: c99ecc4 b3cee61
Author: Andreas Tille <tille at debian.org>
Date: Wed Dec 6 16:01:26 2017 +0100
Updated version 2.1.1+dfsg1 from 'upstream/2.1.1+dfsg1'
with Debian dir 15cc489df6e2e1782e5d8b8602d750348e392224
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(-)
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