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from 001d1dd Update Vcs-* fields to point to the git repository
new 1c238c0 Imported Upstream version 8.1
new 4f73c15 Merge tag 'upstream/8.1'
The 2 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:
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(+)
create mode 120000 samtools
create mode 100644 samtools-0.1.19/.gitignore
create mode 100644 samtools-0.1.19/AUTHORS
create mode 100644 samtools-0.1.19/COPYING
create mode 100644 samtools-0.1.19/ChangeLog.old
create mode 100644 samtools-0.1.19/INSTALL
create mode 100644 samtools-0.1.19/Makefile
create mode 100644 samtools-0.1.19/Makefile.mingw
create mode 100644 samtools-0.1.19/NEWS
create mode 100644 samtools-0.1.19/bam.c
create mode 100644 samtools-0.1.19/bam.h
create mode 100644 samtools-0.1.19/bam2bcf.c
create mode 100644 samtools-0.1.19/bam2bcf.h
create mode 100644 samtools-0.1.19/bam2bcf_indel.c
create mode 100644 samtools-0.1.19/bam2depth.c
create mode 100644 samtools-0.1.19/bam_aux.c
create mode 100644 samtools-0.1.19/bam_cat.c
create mode 100644 samtools-0.1.19/bam_color.c
create mode 100644 samtools-0.1.19/bam_endian.h
create mode 100644 samtools-0.1.19/bam_import.c
create mode 100644 samtools-0.1.19/bam_index.c
create mode 100644 samtools-0.1.19/bam_lpileup.c
create mode 100644 samtools-0.1.19/bam_mate.c
create mode 100644 samtools-0.1.19/bam_md.c
create mode 100644 samtools-0.1.19/bam_pileup.c
create mode 100644 samtools-0.1.19/bam_plcmd.c
create mode 100644 samtools-0.1.19/bam_reheader.c
create mode 100644 samtools-0.1.19/bam_rmdup.c
create mode 100644 samtools-0.1.19/bam_rmdupse.c
create mode 100644 samtools-0.1.19/bam_sort.c
create mode 100644 samtools-0.1.19/bam_stat.c
create mode 100644 samtools-0.1.19/bam_tview.c
create mode 100644 samtools-0.1.19/bam_tview.h
create mode 100644 samtools-0.1.19/bam_tview_curses.c
create mode 100644 samtools-0.1.19/bam_tview_html.c
create mode 100644 samtools-0.1.19/bamshuf.c
create mode 100644 samtools-0.1.19/bamtk.c
create mode 100644 samtools-0.1.19/bcftools/Makefile
create mode 100644 samtools-0.1.19/bcftools/README
create mode 100644 samtools-0.1.19/bcftools/bcf.c
create mode 100644 samtools-0.1.19/bcftools/bcf.h
create mode 100644 samtools-0.1.19/bcftools/bcf.tex
create mode 100644 samtools-0.1.19/bcftools/bcf2qcall.c
create mode 100644 samtools-0.1.19/bcftools/bcfutils.c
create mode 100644 samtools-0.1.19/bcftools/call1.c
create mode 100644 samtools-0.1.19/bcftools/em.c
create mode 100644 samtools-0.1.19/bcftools/fet.c
create mode 100644 samtools-0.1.19/bcftools/index.c
create mode 100644 samtools-0.1.19/bcftools/kfunc.c
create mode 100644 samtools-0.1.19/bcftools/kmin.c
create mode 100644 samtools-0.1.19/bcftools/kmin.h
create mode 100644 samtools-0.1.19/bcftools/main.c
create mode 100644 samtools-0.1.19/bcftools/mut.c
create mode 100644 samtools-0.1.19/bcftools/prob1.c
create mode 100644 samtools-0.1.19/bcftools/prob1.h
create mode 100644 samtools-0.1.19/bcftools/vcf.c
create mode 100755 samtools-0.1.19/bcftools/vcfutils.pl
create mode 100644 samtools-0.1.19/bedcov.c
create mode 100644 samtools-0.1.19/bedidx.c
create mode 100644 samtools-0.1.19/bgzf.c
create mode 100644 samtools-0.1.19/bgzf.h
create mode 100644 samtools-0.1.19/bgzip.c
create mode 100644 samtools-0.1.19/cut_target.c
create mode 100644 samtools-0.1.19/errmod.c
create mode 100644 samtools-0.1.19/errmod.h
create mode 100644 samtools-0.1.19/examples/00README.txt
create mode 100644 samtools-0.1.19/examples/Makefile
create mode 100644 samtools-0.1.19/examples/bam2bed.c
create mode 100644 samtools-0.1.19/examples/calDepth.c
create mode 100644 samtools-0.1.19/examples/chk_indel.c
create mode 100644 samtools-0.1.19/examples/ex1.fa
create mode 100644 samtools-0.1.19/examples/ex1.sam.gz
create mode 100644 samtools-0.1.19/examples/toy.fa
create mode 100644 samtools-0.1.19/examples/toy.sam
create mode 100644 samtools-0.1.19/faidx.c
create mode 100644 samtools-0.1.19/faidx.h
create mode 100644 samtools-0.1.19/kaln.c
create mode 100644 samtools-0.1.19/kaln.h
create mode 100644 samtools-0.1.19/khash.h
create mode 100644 samtools-0.1.19/klist.h
create mode 100644 samtools-0.1.19/knetfile.c
create mode 100644 samtools-0.1.19/knetfile.h
create mode 100644 samtools-0.1.19/kprobaln.c
create mode 100644 samtools-0.1.19/kprobaln.h
create mode 100644 samtools-0.1.19/kseq.h
create mode 100644 samtools-0.1.19/ksort.h
create mode 100644 samtools-0.1.19/kstring.c
create mode 100644 samtools-0.1.19/kstring.h
create mode 100644 samtools-0.1.19/misc/HmmGlocal.java
create mode 100644 samtools-0.1.19/misc/Makefile
create mode 100644 samtools-0.1.19/misc/ace2sam.c
create mode 100644 samtools-0.1.19/misc/bamcheck.c
create mode 100755 samtools-0.1.19/misc/blast2sam.pl
create mode 100755 samtools-0.1.19/misc/bowtie2sam.pl
create mode 100755 samtools-0.1.19/misc/export2sam.pl
create mode 100755 samtools-0.1.19/misc/interpolate_sam.pl
create mode 100644 samtools-0.1.19/misc/maq2sam.c
create mode 100644 samtools-0.1.19/misc/md5.c
create mode 100644 samtools-0.1.19/misc/md5.h
create mode 100644 samtools-0.1.19/misc/md5fa.c
create mode 100755 samtools-0.1.19/misc/novo2sam.pl
create mode 100755 samtools-0.1.19/misc/plot-bamcheck
create mode 100755 samtools-0.1.19/misc/psl2sam.pl
create mode 100755 samtools-0.1.19/misc/r2plot.lua
create mode 100755 samtools-0.1.19/misc/sam2vcf.pl
create mode 100755 samtools-0.1.19/misc/samtools.pl
create mode 100755 samtools-0.1.19/misc/soap2sam.pl
create mode 100755 samtools-0.1.19/misc/varfilter.py
create mode 100755 samtools-0.1.19/misc/vcfutils.lua
create mode 100644 samtools-0.1.19/misc/wgsim.c
create mode 100755 samtools-0.1.19/misc/wgsim_eval.pl
create mode 100755 samtools-0.1.19/misc/zoom2sam.pl
create mode 100644 samtools-0.1.19/padding.c
create mode 100644 samtools-0.1.19/phase.c
create mode 100644 samtools-0.1.19/razf.c
create mode 100644 samtools-0.1.19/razf.h
create mode 100644 samtools-0.1.19/razip.c
create mode 100644 samtools-0.1.19/sam.c
create mode 100644 samtools-0.1.19/sam.h
create mode 100644 samtools-0.1.19/sam_header.c
create mode 100644 samtools-0.1.19/sam_header.h
create mode 100644 samtools-0.1.19/sam_view.c
create mode 100644 samtools-0.1.19/sample.c
create mode 100644 samtools-0.1.19/sample.h
create mode 100644 samtools-0.1.19/samtools.1
create mode 100644 samtools-0.1.19/win32/libcurses.a
create mode 100644 samtools-0.1.19/win32/libz.a
create mode 100644 samtools-0.1.19/win32/xcurses.h
create mode 100644 samtools-0.1.19/win32/zconf.h
create mode 100644 samtools-0.1.19/win32/zlib.h
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