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Commits on Oct 7, 2016

• Place percent mapped bases output in the correct field

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Commits on May 28, 2015

• plot-bamstats: Remove hard-wired 60 columns fasta lines assumption

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Commits on Apr 16, 2015

• Reored usage string

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• Resolved merge conflict

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Commits on Apr 8, 2015

• stats: make cram index work

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Commits on Jan 30, 2015

• Merge pull request samtools#342 from nathanhaigh/develop

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Commits on Nov 3, 2014

• Merge branch 'develop' of github.com:samtools/samtools into develop

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• stats: Calculate mismatches per cycle for unclipped length

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Commits on Oct 21, 2014

• Reflect changes in htslib API

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Commits on Oct 1, 2014

• Merge pull request samtools#306 from jkbonfield/mpileup-fix

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Commits on Sep 5, 2014

• mpileup: conform to VCFv4.2 spec, version string should be quoted

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Commits on Aug 26, 2014

• Clean after fix in e3d4eee

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Commits on Aug 13, 2014

• stats: Compute checksum for names/seqs/quals

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Commits on Aug 12, 2014

• plot-bamstats: fixes in create_html and gz input

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Commits on Aug 11, 2014

• plot-bamstats: Use 0x1 rather than 0x2 flag to detect paired-end

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Commits on Aug 1, 2014

• plot-bamstats: Generate summary html page

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• stats: Accept string flags with -f/F

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Commits on Jul 31, 2014

• plot-bamstats: better support for plots of single-read bams

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Commits on Jul 18, 2014

• mpileup: Support for cigar operation N

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Commits on Jul 10, 2014

• tview: Recover from incomplete fai files

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Commits on Jul 8, 2014

• mpileup: Fix in DPR calculation - there can be

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Commits on Jul 4, 2014

• mpileup: Do not crash on non-existent files, resolves samtools#244

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• mpileup: Support for cigar operator "P", resolves samtools#243

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Commits on Jun 25, 2014

• mpileup: Output symbolic <X> allele instead of VCF-incompatible X

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• mpileup: New optional FORMAT/DPR and INFO/DPR annotations

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Commits on Jun 20, 2014

• Updated calling section of samtools man page

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Commits on Jun 16, 2014

• mpileup tests: Remove temporary hack, view -C -T now works

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Commits on Jun 12, 2014

• mpileup: Reflect change in bcf_hdr_add_sample() usage

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Commits on Jun 2, 2014

• Merge branch 'develop' into QS-vs-PL

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• mpileup: Updated tests

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Commits on May 29, 2014

• mpileup: Per-sample rather than cumulative QS. (experimental)

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Commits on May 20, 2014

• stats: Check for zero-length cigars (e.g. 0D)

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Commits on May 12, 2014

• stats: Simplified usage of --GC-depth, reflen not required

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• mpileup: support for BAM_CHARD_CLIP cigar

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Commits on May 8, 2014

• mpileup: Absolute INFO/QS to allow incremental calling

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