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(parent: 58d504a) | patch
Updated samtools to 0.1.19
authorBo Li <bli@cs.wisc.edu>
Thu, 9 Jan 2014 00:26:18 +0000 (18:26 -0600)
committerBo Li <bli@cs.wisc.edu>
Thu, 9 Jan 2014 00:26:18 +0000 (18:26 -0600)
commitdbcf1cfb8ad1086c21d64e249f012809403e7ddc
treea5f1530588fbe103e1d795cc796fa13f2125d297tree | snapshot
parent58d504aaf36ae486b1dba6d03e0e9f1c25855037commit | diff
Updated samtools to 0.1.19
221 files changed:
EBSeq/BiocInstaller/DESCRIPTION [new file with mode: 0644] blob
EBSeq/BiocInstaller/INDEX [new file with mode: 0644] blob
EBSeq/BiocInstaller/Meta/Rd.rds [new file with mode: 0644] blob
EBSeq/BiocInstaller/Meta/hsearch.rds [new file with mode: 0644] blob
EBSeq/BiocInstaller/Meta/links.rds [new file with mode: 0644] blob
EBSeq/BiocInstaller/Meta/nsInfo.rds [new file with mode: 0644] blob
EBSeq/BiocInstaller/Meta/package.rds [new file with mode: 0644] blob
EBSeq/BiocInstaller/NAMESPACE [new file with mode: 0644] blob
EBSeq/BiocInstaller/NEWS [new file with mode: 0644] blob
EBSeq/BiocInstaller/R/BiocInstaller [new file with mode: 0644] blob
EBSeq/BiocInstaller/R/BiocInstaller.rdb [new file with mode: 0644] blob
EBSeq/BiocInstaller/R/BiocInstaller.rdx [new file with mode: 0644] blob
EBSeq/BiocInstaller/help/AnIndex [new file with mode: 0644] blob
EBSeq/BiocInstaller/help/BiocInstaller.rdb [new file with mode: 0644] blob
EBSeq/BiocInstaller/help/BiocInstaller.rdx [new file with mode: 0644] blob
EBSeq/BiocInstaller/help/aliases.rds [new file with mode: 0644] blob
EBSeq/BiocInstaller/help/paths.rds [new file with mode: 0644] blob
EBSeq/BiocInstaller/html/00Index.html [new file with mode: 0644] blob
EBSeq/BiocInstaller/html/R.css [new file with mode: 0644] blob
EBSeq/BiocInstaller/scripts/biocLite.R [new file with mode: 0644] blob
EBSeq/BiocInstaller/unitTests/test_BiocUpgrade.R [new file with mode: 0644] blob
EBSeq/BiocInstaller/unitTests/test_biocinstallRepos.R [new file with mode: 0644] blob
EBSeq/calcClusteringInfo.cpp diff | blob | history
README.md diff | blob | history
ReadReader.h diff | blob | history
Refs.h diff | blob | history
extractRef.cpp diff | blob | history
makefile diff | blob | history
sam/.DS_Store [new file with mode: 0644] blob
sam/._.DS_Store [new file with mode: 0644] blob
sam/._.gitignore [new file with mode: 0644] blob
sam/._AUTHORS [new file with mode: 0644] blob
sam/._COPYING [new file with mode: 0644] blob
sam/._ChangeLog.old [new file with mode: 0644] blob
sam/._INSTALL [new file with mode: 0644] blob
sam/._Makefile.mingw [new file with mode: 0644] blob
sam/._NEWS [new file with mode: 0644] blob
sam/._bam.c [new file with mode: 0644] blob
sam/._bam.h [new file with mode: 0644] blob
sam/._bam2bcf.c [new file with mode: 0644] blob
sam/._bam2bcf.h [new file with mode: 0644] blob
sam/._bam2bcf_indel.c [new file with mode: 0644] blob
sam/._bam2depth.c [new file with mode: 0644] blob
sam/._bam_aux.c [new file with mode: 0644] blob
sam/._bam_cat.c [new file with mode: 0644] blob
sam/._bam_color.c [new file with mode: 0644] blob
sam/._bam_endian.h [new file with mode: 0644] blob
sam/._bam_import.c [new file with mode: 0644] blob
sam/._bam_index.c [new file with mode: 0644] blob
sam/._bam_lpileup.c [new file with mode: 0644] blob
sam/._bam_mate.c [new file with mode: 0644] blob
sam/._bam_md.c [new file with mode: 0644] blob
sam/._bam_pileup.c [new file with mode: 0644] blob
sam/._bam_plcmd.c [new file with mode: 0644] blob
sam/._bam_reheader.c [new file with mode: 0644] blob
sam/._bam_rmdup.c [new file with mode: 0644] blob
sam/._bam_rmdupse.c [new file with mode: 0644] blob
sam/._bam_sort.c [new file with mode: 0644] blob
sam/._bam_stat.c [new file with mode: 0644] blob
sam/._bam_tview.c [new file with mode: 0644] blob
sam/._bam_tview.h [new file with mode: 0644] blob
sam/._bam_tview_curses.c [new file with mode: 0644] blob
sam/._bam_tview_html.c [new file with mode: 0644] blob
sam/._bamshuf.c [new file with mode: 0644] blob
sam/._bamtk.c [new file with mode: 0644] blob
sam/._bcftools [new file with mode: 0755] blob
sam/._bedcov.c [new file with mode: 0644] blob
sam/._bedidx.c [new file with mode: 0644] blob
sam/._bgzf.c [new file with mode: 0644] blob
sam/._bgzf.h [new file with mode: 0644] blob
sam/._bgzip.c [new file with mode: 0644] blob
sam/._cut_target.c [new file with mode: 0644] blob
sam/._errmod.c [new file with mode: 0644] blob
sam/._errmod.h [new file with mode: 0644] blob
sam/._examples [new file with mode: 0755] blob
sam/._faidx.c [new file with mode: 0644] blob
sam/._faidx.h [new file with mode: 0644] blob
sam/._kaln.c [new file with mode: 0644] blob
sam/._kaln.h [new file with mode: 0644] blob
sam/._khash.h [new file with mode: 0644] blob
sam/._klist.h [new file with mode: 0644] blob
sam/._knetfile.c [new file with mode: 0644] blob
sam/._knetfile.h [new file with mode: 0644] blob
sam/._kprobaln.c [new file with mode: 0644] blob
sam/._kprobaln.h [new file with mode: 0644] blob
sam/._kseq.h [new file with mode: 0644] blob
sam/._ksort.h [new file with mode: 0644] blob
sam/._kstring.c [new file with mode: 0644] blob
sam/._kstring.h [new file with mode: 0644] blob
sam/._misc [new file with mode: 0755] blob
sam/._padding.c [new file with mode: 0644] blob
sam/._phase.c [new file with mode: 0644] blob
sam/._razf.c [new file with mode: 0644] blob
sam/._razf.h [new file with mode: 0644] blob
sam/._razip.c [new file with mode: 0644] blob
sam/._sam.c [new file with mode: 0644] blob
sam/._sam.h [new file with mode: 0644] blob
sam/._sam_header.c [new file with mode: 0644] blob
sam/._sam_header.h [new file with mode: 0644] blob
sam/._sam_view.c [new file with mode: 0644] blob
sam/._sample.c [new file with mode: 0644] blob
sam/._sample.h [new file with mode: 0644] blob
sam/._samtools.1 [new file with mode: 0644] blob
sam/._win32 [new file with mode: 0755] blob
sam/ChangeLog [deleted file] blob | history
sam/ChangeLog.old [new file with mode: 0644] blob
sam/Makefile diff | blob | history
sam/NEWS diff | blob | history
sam/bam.c diff | blob | history
sam/bam.h diff | blob | history
sam/bam2bcf.c diff | blob | history
sam/bam2bcf.h diff | blob | history
sam/bam2bcf_indel.c diff | blob | history
sam/bam2depth.c diff | blob | history
sam/bam_aux.c diff | blob | history
sam/bam_cat.c diff | blob | history
sam/bam_color.c diff | blob | history
sam/bam_import.c diff | blob | history
sam/bam_index.c diff | blob | history
sam/bam_mate.c diff | blob | history
sam/bam_md.c diff | blob | history
sam/bam_plcmd.c diff | blob | history
sam/bam_reheader.c diff | blob | history
sam/bam_sort.c diff | blob | history
sam/bam_tview.c diff | blob | history
sam/bam_tview.h [new file with mode: 0644] blob
sam/bam_tview_curses.c [new file with mode: 0644] blob
sam/bam_tview_html.c [new file with mode: 0644] blob
sam/bamshuf.c [new file with mode: 0644] blob
sam/bamtk.c diff | blob | history
sam/bcftools/._Makefile [new file with mode: 0644] blob
sam/bcftools/._README [new file with mode: 0644] blob
sam/bcftools/._bcf.c [new file with mode: 0644] blob
sam/bcftools/._bcf.h [new file with mode: 0644] blob
sam/bcftools/._bcf.tex [new file with mode: 0644] blob
sam/bcftools/._bcf2qcall.c [new file with mode: 0644] blob
sam/bcftools/._bcfutils.c [new file with mode: 0644] blob
sam/bcftools/._call1.c [new file with mode: 0644] blob
sam/bcftools/._em.c [new file with mode: 0644] blob
sam/bcftools/._fet.c [new file with mode: 0644] blob
sam/bcftools/._index.c [new file with mode: 0644] blob
sam/bcftools/._kfunc.c [new file with mode: 0644] blob
sam/bcftools/._kmin.c [new file with mode: 0644] blob
sam/bcftools/._kmin.h [new file with mode: 0644] blob
sam/bcftools/._main.c [new file with mode: 0644] blob
sam/bcftools/._mut.c [new file with mode: 0644] blob
sam/bcftools/._prob1.c [new file with mode: 0644] blob
sam/bcftools/._prob1.h [new file with mode: 0644] blob
sam/bcftools/._vcf.c [new file with mode: 0644] blob
sam/bcftools/._vcfutils.pl [new file with mode: 0755] blob
sam/bcftools/Makefile diff | blob | history
sam/bcftools/bcf.c diff | blob | history
sam/bcftools/bcf.h diff | blob | history
sam/bcftools/bcfutils.c diff | blob | history
sam/bcftools/call1.c diff | blob | history
sam/bcftools/index.c diff | blob | history
sam/bcftools/main.c diff | blob | history
sam/bcftools/prob1.c diff | blob | history
sam/bcftools/prob1.h diff | blob | history
sam/bcftools/vcf.c diff | blob | history
sam/bedcov.c [new file with mode: 0644] blob
sam/bgzf.c diff | blob | history
sam/bgzf.h diff | blob | history
sam/examples/._00README.txt [new file with mode: 0644] blob
sam/examples/._Makefile [new file with mode: 0644] blob
sam/examples/._bam2bed.c [new file with mode: 0644] blob
sam/examples/._calDepth.c [new file with mode: 0644] blob
sam/examples/._chk_indel.c [new file with mode: 0644] blob
sam/examples/._ex1.fa [new file with mode: 0644] blob
sam/examples/._ex1.sam.gz [new file with mode: 0644] blob
sam/examples/._toy.fa [new file with mode: 0644] blob
sam/examples/._toy.sam [new file with mode: 0644] blob
sam/examples/chk_indel.c [new file with mode: 0644] blob
sam/faidx.c diff | blob | history
sam/kprobaln.c diff | blob | history
sam/kseq.h diff | blob | history
sam/ksort.h diff | blob | history
sam/kstring.c diff | blob | history
sam/kstring.h diff | blob | history
sam/misc/._HmmGlocal.java [new file with mode: 0644] blob
sam/misc/._Makefile [new file with mode: 0644] blob
sam/misc/._ace2sam.c [new file with mode: 0644] blob
sam/misc/._bamcheck.c [new file with mode: 0644] blob
sam/misc/._blast2sam.pl [new file with mode: 0755] blob
sam/misc/._bowtie2sam.pl [new file with mode: 0755] blob
sam/misc/._export2sam.pl [new file with mode: 0755] blob
sam/misc/._interpolate_sam.pl [new file with mode: 0755] blob
sam/misc/._maq2sam.c [new file with mode: 0644] blob
sam/misc/._md5.c [new file with mode: 0644] blob
sam/misc/._md5.h [new file with mode: 0644] blob
sam/misc/._md5fa.c [new file with mode: 0644] blob
sam/misc/._novo2sam.pl [new file with mode: 0755] blob
sam/misc/._plot-bamcheck [new file with mode: 0755] blob
sam/misc/._psl2sam.pl [new file with mode: 0755] blob
sam/misc/._r2plot.lua [new file with mode: 0755] blob
sam/misc/._sam2vcf.pl [new file with mode: 0755] blob
sam/misc/._samtools.pl [new file with mode: 0755] blob
sam/misc/._soap2sam.pl [new file with mode: 0755] blob
sam/misc/._varfilter.py [new file with mode: 0755] blob
sam/misc/._vcfutils.lua [new file with mode: 0755] blob
sam/misc/._wgsim.c [new file with mode: 0644] blob
sam/misc/._wgsim_eval.pl [new file with mode: 0755] blob
sam/misc/._zoom2sam.pl [new file with mode: 0755] blob
sam/misc/Makefile diff | blob | history
sam/misc/ace2sam.c [new file with mode: 0644] blob
sam/misc/bamcheck.c [new file with mode: 0644] blob
sam/misc/plot-bamcheck [new file with mode: 0755] blob
sam/misc/r2plot.lua [new file with mode: 0755] blob
sam/misc/seqtk.c [deleted file] blob | history
sam/misc/vcfutils.lua [new file with mode: 0755] blob
sam/padding.c [new file with mode: 0644] blob
sam/sam.c diff | blob | history
sam/sam.h diff | blob | history
sam/sam_header.c diff | blob | history
sam/sam_header.h diff | blob | history
sam/sam_view.c diff | blob | history
sam/samtools.1 diff | blob | history
sam/win32/._xcurses.h [new file with mode: 0644] blob
sam/win32/._zconf.h [new file with mode: 0644] blob
sam/win32/._zlib.h [new file with mode: 0644] blob
synthesisRef.cpp diff | blob | history
Debian packaging of rsem