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1. Commits on Oct 28, 2015

   • Fix GT splitting in bcftools norm

     jpiper

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2. Commits on Oct 22, 2015

   • norm: Expand round buffer if needed. Fixes #336

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     pd3

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     mcshane

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   • add test for consensus on empty vcf file

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     mcshane

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3. Commits on Oct 15, 2015

   • Merge pull request #337 from adamspargo/issue320

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     mcshane

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   • change to filter.c:filters_init()

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     adamspargo

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   • New hidden -n and -S options to polysomy

     

     pd3

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     mcshane

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   • Small polysomy improvements

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     pd3

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     mcshane

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   • genaralise mcall_trim_numberR beyond DPR to any Number=R/Type=Integer tag

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     mcshane

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4. Commits on Oct 12, 2015

   • add tests for trimming many alleles and dropping header+format

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     mcshane

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5. Commits on Oct 2, 2015

   • rename plugin/info.c -> plugin/impute-info.c

     mcshane

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   • Makefile: remove unnecessary "\"

     mcshane

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   • color-chrs.pl: add copyright boilerplate

     mcshane

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   • tag2tag.c: minor fix to boilerplate header

     mcshane

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   • add plugin to color shared chromosomal segments

     mcshane

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   • mendelian plugin to check for mendelian inconsistencies

     mcshane

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   • add info plugin to add information metrics from GP tags

     mcshane

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6. Commits on Oct 1, 2015

   • docs: clarify merge behaviour for INFO and QUAL fields

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     mcshane

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   • Merge branch 'wkretzsch-develop' into develop

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   • vcfconvert: support for END tag when converting from oxford formats to VCF

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     mcshane

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   • Merge branch 'develop' of https://github.com/wkretzsch/bcftools into wkretzsch-develop

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   • vcfcall: gvcf calling not working with -c calling mode yet

     mcshane

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7. Commits on Sep 30, 2015

   • Bringing "call --gvcf" from experimental to main repo.

     

     pd3

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     mcshane

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   • vcfindex: make index -s work even if length attribute is not present

     

     pd3

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8. Commits on Sep 25, 2015

   • Fixed bug in trio calling introduced by bcc7b26e

     

     pd3

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     mcshane

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9. Commits on Sep 24, 2015

   • Merge pull request #321 from humanlongevity/develop

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     mcshane

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10. Commits on Sep 22, 2015

    • convert -H: Fixes issue #274; adds support for haploid and missing alleles

      winni2k

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11. Commits on Sep 17, 2015

    • Update test VCF headers to v4.2

      

      Jason Piper

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      Jason Piper

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12. Commits on Sep 16, 2015

    • convert: Report the number of written records

      

      pd3

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      mcshane

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    • fixploidy: Do not exit on lines without GT, leave unchanged

      

      pd3

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      mcshane

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    • Plugins to use bcf_gt_is_missing instead of the old bcf_int32_missing

      

      pd3

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      mcshane

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    • new setGT plugin

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      mcshane

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    • PL to determine sex with +vcf2sex

      mcshane

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13. Commits on Sep 15, 2015

    • docs: mention that --fasta-ref is required for left-alignment and normalization

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      mcshane

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    • plot-vcfstats: ensure merged SN fields are in a specific order

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      mcshane

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14. Commits on Sep 14, 2015

    • Merge norm -m- test (PR #315)

      jmarshall

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