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commit 4f73c15c1c2ad934b4b8047fb6d4ddae26acf7f2
Merge: 001d1dd 1c238c0
Author: Afif Elghraoui <a...@ghraoui.name>
Date: Sat May 2 23:01:46 2015 -0700
Merge tag 'upstream/8.1'
Upstream version 8.1
samtools | 1 +
samtools-0.1.19/.gitignore | 4 +
samtools-0.1.19/AUTHORS | 20 +
samtools-0.1.19/COPYING | 21 +
samtools-0.1.19/ChangeLog.old | 3875 +++++++++++++++++++++++++++++++
samtools-0.1.19/INSTALL | 30 +
samtools-0.1.19/Makefile | 101 +
samtools-0.1.19/Makefile.mingw | 63 +
samtools-0.1.19/NEWS | 836 +++++++
samtools-0.1.19/bam.c | 474 ++++
samtools-0.1.19/bam.h | 793 +++++++
samtools-0.1.19/bam2bcf.c | 467 ++++
samtools-0.1.19/bam2bcf.h | 67 +
samtools-0.1.19/bam2bcf_indel.c | 498 ++++
samtools-0.1.19/bam2depth.c | 143 ++
samtools-0.1.19/bam_aux.c | 217 ++
samtools-0.1.19/bam_cat.c | 185 ++
samtools-0.1.19/bam_color.c | 145 ++
samtools-0.1.19/bam_endian.h | 42 +
samtools-0.1.19/bam_import.c | 489 ++++
samtools-0.1.19/bam_index.c | 726 ++++++
samtools-0.1.19/bam_lpileup.c | 198 ++
samtools-0.1.19/bam_mate.c | 128 +
samtools-0.1.19/bam_md.c | 389 ++++
samtools-0.1.19/bam_pileup.c | 437 ++++
samtools-0.1.19/bam_plcmd.c | 606 +++++
samtools-0.1.19/bam_reheader.c | 62 +
samtools-0.1.19/bam_rmdup.c | 206 ++
samtools-0.1.19/bam_rmdupse.c | 159 ++
samtools-0.1.19/bam_sort.c | 571 +++++
samtools-0.1.19/bam_stat.c | 77 +
samtools-0.1.19/bam_tview.c | 368 +++
samtools-0.1.19/bam_tview.h | 75 +
samtools-0.1.19/bam_tview_curses.c | 297 +++
samtools-0.1.19/bam_tview_html.c | 349 +++
samtools-0.1.19/bamshuf.c | 141 ++
samtools-0.1.19/bamtk.c | 119 +
samtools-0.1.19/bcftools/Makefile | 51 +
samtools-0.1.19/bcftools/README | 36 +
samtools-0.1.19/bcftools/bcf.c | 396 ++++
samtools-0.1.19/bcftools/bcf.h | 197 ++
samtools-0.1.19/bcftools/bcf.tex | 77 +
samtools-0.1.19/bcftools/bcf2qcall.c | 91 +
samtools-0.1.19/bcftools/bcfutils.c | 504 ++++
samtools-0.1.19/bcftools/call1.c | 633 +++++
samtools-0.1.19/bcftools/em.c | 310 +++
samtools-0.1.19/bcftools/fet.c | 112 +
samtools-0.1.19/bcftools/index.c | 336 +++
samtools-0.1.19/bcftools/kfunc.c | 162 ++
samtools-0.1.19/bcftools/kmin.c | 209 ++
samtools-0.1.19/bcftools/kmin.h | 46 +
samtools-0.1.19/bcftools/main.c | 191 ++
samtools-0.1.19/bcftools/mut.c | 127 +
samtools-0.1.19/bcftools/prob1.c | 988 ++++++++
samtools-0.1.19/bcftools/prob1.h | 49 +
samtools-0.1.19/bcftools/vcf.c | 249 ++
samtools-0.1.19/bcftools/vcfutils.pl | 567 +++++
samtools-0.1.19/bedcov.c | 127 +
samtools-0.1.19/bedidx.c | 162 ++
samtools-0.1.19/bgzf.c | 694 ++++++
samtools-0.1.19/bgzf.h | 207 ++
samtools-0.1.19/bgzip.c | 206 ++
samtools-0.1.19/cut_target.c | 193 ++
samtools-0.1.19/errmod.c | 130 ++
samtools-0.1.19/errmod.h | 24 +
samtools-0.1.19/examples/00README.txt | 23 +
samtools-0.1.19/examples/Makefile | 50 +
samtools-0.1.19/examples/bam2bed.c | 51 +
samtools-0.1.19/examples/calDepth.c | 62 +
samtools-0.1.19/examples/chk_indel.c | 83 +
samtools-0.1.19/examples/ex1.fa | 56 +
samtools-0.1.19/examples/ex1.sam.gz | Bin 0 -> 114565 bytes
samtools-0.1.19/examples/toy.fa | 4 +
samtools-0.1.19/examples/toy.sam | 14 +
samtools-0.1.19/faidx.c | 437 ++++
samtools-0.1.19/faidx.h | 103 +
samtools-0.1.19/kaln.c | 486 ++++
samtools-0.1.19/kaln.h | 67 +
samtools-0.1.19/khash.h | 528 +++++
samtools-0.1.19/klist.h | 96 +
samtools-0.1.19/knetfile.c | 632 +++++
samtools-0.1.19/knetfile.h | 75 +
samtools-0.1.19/kprobaln.c | 280 +++
samtools-0.1.19/kprobaln.h | 49 +
samtools-0.1.19/kseq.h | 235 ++
samtools-0.1.19/ksort.h | 285 +++
samtools-0.1.19/kstring.c | 212 ++
samtools-0.1.19/kstring.h | 169 ++
samtools-0.1.19/misc/HmmGlocal.java | 178 ++
samtools-0.1.19/misc/Makefile | 69 +
samtools-0.1.19/misc/ace2sam.c | 249 ++
samtools-0.1.19/misc/bamcheck.c | 1521 ++++++++++++
samtools-0.1.19/misc/blast2sam.pl | 92 +
samtools-0.1.19/misc/bowtie2sam.pl | 92 +
samtools-0.1.19/misc/export2sam.pl | 545 +++++
samtools-0.1.19/misc/interpolate_sam.pl | 125 +
samtools-0.1.19/misc/maq2sam.c | 173 ++
samtools-0.1.19/misc/md5.c | 296 +++
samtools-0.1.19/misc/md5.h | 57 +
samtools-0.1.19/misc/md5fa.c | 58 +
samtools-0.1.19/misc/novo2sam.pl | 281 +++
samtools-0.1.19/misc/plot-bamcheck | 882 +++++++
samtools-0.1.19/misc/psl2sam.pl | 65 +
samtools-0.1.19/misc/r2plot.lua | 83 +
samtools-0.1.19/misc/sam2vcf.pl | 270 +++
samtools-0.1.19/misc/samtools.pl | 528 +++++
samtools-0.1.19/misc/soap2sam.pl | 109 +
samtools-0.1.19/misc/varfilter.py | 205 ++
samtools-0.1.19/misc/vcfutils.lua | 694 ++++++
samtools-0.1.19/misc/wgsim.c | 419 ++++
samtools-0.1.19/misc/wgsim_eval.pl | 91 +
samtools-0.1.19/misc/zoom2sam.pl | 97 +
samtools-0.1.19/padding.c | 479 ++++
samtools-0.1.19/phase.c | 687 ++++++
samtools-0.1.19/razf.c | 853 +++++++
samtools-0.1.19/razf.h | 134 ++
samtools-0.1.19/razip.c | 141 ++
samtools-0.1.19/sam.c | 186 ++
samtools-0.1.19/sam.h | 99 +
samtools-0.1.19/sam_header.c | 810 +++++++
samtools-0.1.19/sam_header.h | 48 +
samtools-0.1.19/sam_view.c | 441 ++++
samtools-0.1.19/sample.c | 107 +
samtools-0.1.19/sample.h | 17 +
samtools-0.1.19/samtools.1 | 1066 +++++++++
samtools-0.1.19/win32/libcurses.a | Bin 0 -> 114764 bytes
samtools-0.1.19/win32/libz.a | Bin 0 -> 74266 bytes
samtools-0.1.19/win32/xcurses.h | 1377 +++++++++++
samtools-0.1.19/win32/zconf.h | 332 +++
samtools-0.1.19/win32/zlib.h | 1357 +++++++++++
130 files changed, 39763 insertions(+)
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