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Commits on Apr 22, 2015

• change allele dosage annotation from AD to ADS to avoid collision with GATK allele depth

  mcshane

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  6662992

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• set htslib=1.2.1, pbwt=3.1 and link against bsd

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  baffe47

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Commits on Feb 27, 2015

• treat a null (.) allele as match when selecting sites

  mcshane

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  26c1ed3

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• convert ref/alt to uppercase when reading in VCF

  mcshane

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  97bd487

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• bugfix so that pbwt does not crash when reading a VCF site with no ALT allele

  mcshane

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  bd353a2

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Commits on Feb 12, 2015

• include dosages when -readAll

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  de43336

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Commits on Feb 11, 2015

• little bit cleaner?

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  2c54482

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• add comment about double vs float for dosages vs bcf

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  0038144

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• write dosages in VCF output

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  70a80a3

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Commits on Feb 9, 2015

• if available, use dosages when wriring GEN files

  mcshane

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  723e5fb

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• print the version in main command help including git hash if available; print command line and version to vcf header on output

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  2cd7f22

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Commits on Nov 13, 2014

• Merge branch 'master' of github.com:richarddurbin/pbwt into feature/test_referenceImpute

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  d06ad23

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• Merge branch 'master' of github.com:richarddurbin/pbwt into feature/writeBcf

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  7d97941

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Commits on Oct 10, 2014

• try to match RD coding style

  mcshane

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  12b6d7c

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• remove some strange local file that got committed

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  b7c4c02

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• update bcf alleles

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  committed
  1eccb15

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• add -writeVcfGz and condense -writeVcf etc usage messages

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  637efd2

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• match style for variable names

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  f81c3a8

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Commits on Oct 9, 2014

• build up bcf record directly rather then via vcf_parse

  mcshane

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  3753b75

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• add support for writing BCF

  mcshane

  committed
  7a6f939

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• add test for referenceImpute

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  d125c22

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Commits on Sep 23, 2014

• bugfix for a corner case in matchSequencesSweep

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  667d03f

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Commits on Apr 29, 2014

• readVcfGT: split non-biallelic records rather then skipping

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  68835fc

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Commits on Mar 3, 2014

• update for latest htslib API

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  9d4e00d

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Commits on Feb 28, 2014

• advertise -writeVcf in the help message

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  3e8027f

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Commits on Jan 2, 2014

• free allocated memory to keep valgrind happy

  mcshane

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  02dcfe4

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• changes to let tests pass since addition of aFend. also readSites file was not storing variation correctly

  mcshane

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  b587529

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• add test for writeVcf

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  2391e23

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• add ability to write out VCF using htslib

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  0a7a1cf

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• add .PHONY to makefile so make test actually runs the tests

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  ef7733f

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