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Tools (written in C using htslib) for manipulating next-generation sequencing data
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.travis Travis builds clone corresponding htslib branch
examples Update 00README.txt
misc added pipe input support to plot-bamstats: use "-" as the bamcheck fi…
test Merge @CO headers
win32 * samtools-0.1.5-22 (r432)
.gitattributes Travis builds clone corresponding htslib branch
.gitignore Replace bcftools+bcf_filter.sh with new vcf-miniview
.travis.yml Travis builds clone corresponding htslib branch
AUTHORS Remove razip source code and remaining vestiges
ChangeLog.old Removed SVN ChangeLog; merged my private github Log to ChangeLog.old
INSTALL Fix typo.
LICENSE Update license file
Makefile Added "samtools depth" check outputs to testclean target
Makefile.mingw for WIN32 compatibility
NEWS Add samtools 1.0 faidx RAZF->BGZF note
README Added pointer to our own published zlib benchmarks.
README.md Merge #148, links to 'sister' projects (but omitting ourself)
bam.c Reduce use of abort, remove assert(fp), pass one string to fprintf no…
bam.h Add sam_index_load() and samfetch() to legacy API
bam2bcf.c Replace bam_nt16_nt4_table[] by htslib's seq_nt16_int[]
bam2bcf.h Do min_frac comparisons as double rather than float
bam2bcf_indel.c Do min_frac comparisons as double rather than float
bam2depth.c Reored usage string
bam_aux.c Handle hts_parse_reg() returning NULL
bam_cat.c Update copyright years and reformat licensing boilerplate
bam_color.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
bam_endian.h Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
bam_flags.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
bam_import.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
bam_index.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
bam_lpileup.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
bam_lpileup.h Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
bam_mate.c For 0.1.x compatibility, "fixmate - -" writes BAM
bam_md.c Fix calmd -u to write level-0-compressed rather than raw BAM
bam_plbuf.c Reduce use of abort, remove assert(fp), pass one string to fprintf no…
bam_plbuf.h Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
bam_plcmd.c Regression.sh fix and mpileup hts_set_fai_filename fix.
bam_reheader.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
bam_rmdup.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
bam_rmdupse.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
bam_sort.c Merge @CO headers
bam_split.c Reduce use of abort, remove assert(fp), pass one string to fprintf no…
bam_stat.c [flagstat] Print "N/A" rather than NaN percentages
bam_tview.c Handle hts_parse_reg() returning NULL
bam_tview.h Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
bam_tview_curses.c Handle hts_parse_reg() returning NULL
bam_tview_html.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
bamshuf.c Merge abort/assert reduction (PR #290)
bamtk.c samtools dict command to create a sequence dictionary file from a fasta
bedcov.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
bedidx.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
cut_target.c Replace bam_nt16_nt4_table[] by htslib's seq_nt16_int[]
dict.c Merge new dict command (PR #366)
errmod.c Add a few comments to pileup and errmod code, move some existing ones…
errmod.h Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
faidx.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
kprobaln.c Update copyright years to reflect historic changes
kprobaln.h Update copyright years to reflect historic changes
padding.c Prevent warnings when compiling on a 32-bit host [minor]
phase.c Replace bam_nt16_nt4_table[] by htslib's seq_nt16_int[]
sam.c Add sam_index_load() and samfetch() to legacy API
sam.h Add sam_index_load() and samfetch() to legacy API
sam_header.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
sam_header.h Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
sam_view.c Merge bam2fq RG/BC/QT copying (PR #325)
sample.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
sample.h Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
samtools.1 allow samtools merge with one input file
samtools.h Add copyright notices and licensing boilerplate
stats.c stats: make cram index work
stats_isize.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
stats_isize.h Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT

README.md

samtools

This is the official development repository for samtools.

The original samtools package has been split into three separate but tightly coordinated projects:

  • htslib: C-library for handling high-throughput sequencing data
  • samtools: mpileup and other tools for handling SAM, BAM, CRAM
  • bcftools: calling and other tools for handling VCF, BCF

See also http://github.com/samtools/

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