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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 Merge use of htslib's MD5 API (PR #354)
test Swapped bam for sam in samtools depth tests.
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 Release 1.2: various bug fixes
README Release 1.2: various bug fixes
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 fix DPR annotation
bam2bcf_indel.c Replace bam_nt16_nt4_table[] by htslib's seq_nt16_int[]
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 Make bam_merge_core2 check that sam_index_load() worked.
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 add bam2fq -t option to man page
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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