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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

  committed
  6662992

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

  mcshane

  committed
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Commits on Mar 13, 2015

• revised 4hapstats

  richarddurbin

  committed
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Commits on Mar 12, 2015

• Merge pull request richarddurbin#27 from mcshane/feature/uncalled_vcf_sites

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  richarddurbin

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Commits on Mar 1, 2015

• Merge pull request richarddurbin#25 from mcshane/feature/readAllDosages

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  richarddurbin

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• Merge pull request richarddurbin#24 from mcshane/feature/version2

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  richarddurbin

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• Merge pull request richarddurbin#23 from mcshane/feature/writeGen

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  richarddurbin

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• Merge pull request richarddurbin#22 from mcshane/feature/writeVCFdosage

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  richarddurbin

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Commits on Feb 27, 2015

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

  mcshane

  committed
  26c1ed3

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• convert ref/alt to uppercase when reading in VCF

  mcshane

  committed
  97bd487

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

  mcshane

  committed
  bd353a2

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Commits on Feb 12, 2015

• include dosages when -readAll

  mcshane

  committed
  de43336

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Commits on Feb 11, 2015

• little bit cleaner?

  mcshane

  committed
  2c54482

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• add comment about double vs float for dosages vs bcf

  mcshane

  committed
  0038144

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• write dosages in VCF output

  mcshane

  committed
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Commits on Feb 9, 2015

• if available, use dosages when wriring GEN files

  mcshane

  committed
  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

  mcshane

  committed
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Commits on Feb 5, 2015

• compile warning cleanup

  richarddurbin

  committed
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• added nSparse, fSparse to ReferenceImpute, using SweepSparse in pbwtMatch.c

  richarddurbin

  committed
  9e1a51b

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• add errno.h

  richarddurbin

  committed
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Commits on Jan 11, 2015

• Merge pull request richarddurbin#21 from danjlawson/master

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  richarddurbin

  committed
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• fix to dosageStore

  richarddurbin

  committed
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Commits on Dec 28, 2014

• paintSparse added

  danjlawson

  committed
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Commits on Nov 13, 2014

• updated info in vcf file

  richarddurbin

  committed
  d5cf263

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• replace error() by die()

  richarddurbin

  committed
  a7c2cb5

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• Merge pull request richarddurbin#19 from mcshane/feature/writeBcf

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  richarddurbin

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• Merge pull request richarddurbin#18 from mcshane/feature/test_referenceImpute

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  richarddurbin

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

  mcshane

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

  mcshane

  committed
  7d97941

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• fix merge conflicts

  richarddurbin

  committed
  26875fd

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• write sites.freq in option -sfs, and add code to read reference site frequencies and use them in genotypeCompare

  richarddurbin

  committed
  fc2de23

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• correct hreshold for imputation from 0.2 to 0.55

  richarddurbin

  committed
  8143e96

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• restructure a bit and add pbwtGeneticMap.c

  richarddurbin

  committed
  f64b39e

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• add dosage handling, commandLine storing, genetic map handling

  richarddurbin

  committed
  ac2dfdc

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• new functions to read and use genetic map (Oxford style)

  richarddurbin

  committed
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