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Tools (written in C using htslib) for manipulating next-generation sequencing data

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bcftools
examples another example, used by g1k for QA
misc
win32 * samtools-0.1.5-22 (r432)
.gitignore added .gitignore
AUTHORS Improved efficiency of header parsing
COPYING * Merge from branches/dev/
ChangeLog.old Removed SVN ChangeLog; merged my private github Log to ChangeLog.old
INSTALL * avoid a segfault when network connect fails
Makefile
Makefile.mingw for WIN32 compatibility
NEWS
bam.c changes from git
bam.h
bam2bcf.c
bam2bcf.h
bam2bcf_indel.c
bam2depth.c
bam_aux.c
bam_cat.c updated with the latest bgzf library
bam_color.c Incoporated changes from Nils Homer.
bam_endian.h Create trunk copy
bam_import.c changes from git
bam_index.c
bam_lpileup.c * samtools-0.1.5-5 (r395)
bam_mate.c
bam_md.c The -E switch to recalculate extended BAQ on the fly, ignoring existi…
bam_pileup.c * Updated samtools to the latest
bam_plcmd.c
bam_reheader.c updated with the latest bgzf library
bam_rmdup.c * This revision is SERIOUSLY BUGGY. Please NOT use it.
bam_rmdupse.c * This revision is SERIOUSLY BUGGY. Please NOT use it.
bam_sort.c
bam_stat.c Release samtools-0.1.15 (r949:203)
bam_tview.c
bamshuf.c change the default clevel to 1 for speed
bamtk.c added bamshuf from htslib
bedcov.c
bedidx.c for WIN32 compatibility
bgzf.c bugfix: bgzf-mt may write prematured output
bgzf.h compiling errors on some machines
bgzip.c
cut_target.c * change the order of PL/GL according to the latest VCF spec
errmod.c added revised MAQ error model
errmod.h added the phase command
faidx.c
faidx.h * samtools-0.1.6-2 (r458)
kaln.c indel calling is apparently working, but more information needs to be…
kaln.h prepare for the indel caller. It is not ready yet.
khash.h added the phase command
klist.h * samtools-0.1.6-15 (r482)
knetfile.c * avoid a segfault when network connect fails
knetfile.h * samtools-0.1.6-9 (r470)
kprobaln.c Temporary fix to prevent segfault in kpa_glocal
kprobaln.h * prepare to replace kaln with kprobaln in realignment
kseq.h updated to the latest kseq
ksort.h support trio indels
kstring.c converted padded SAM to unpadded SAM
kstring.h r572: added "bedcov" command
padding.c
phase.c * optionally drop phase ambiguous reads
razf.c Bug fix - faidx on RAZF compressed files now working.
razf.h * samtools-0.1.6-5 (r462)
razip.c * fixed a bug in razip: -c will delete the input file
sam.c multi-threading working on toy examples
sam.h multi-threading working on toy examples
sam_header.c
sam_header.h
sam_view.c
sample.c * bugfix in index: large memory when a read pos is 1
sample.h * samtools-0.1.8-13 (r715)
samtools.1
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