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Commits on Apr 22, 2015

• add tests for mendelian error

  brentp

  committed
  d510e2b

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• update comphet tests

  brentp

  committed
  e454579

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• update de-novo tests for new format

  brentp

  committed
  580bf7d

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• update auto-rec tests for new format

  brentp

  committed
  b928c03

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• update auto-dom tests for new format

  brentp

  committed
  8563a0e

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• bed output for stuff from inheritance factory

  brentp

  committed
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Commits on Apr 6, 2015

• Merge pull request #429 from brentp/genotype-likelihoods

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  arq5x

  committed
  b02f8d9

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• add more tests and document changes to database schema

  brentp

  committed
  8fd66c5

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• split likelihoods to homref, het, homalt cols

  brentp

  committed
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Commits on Apr 2, 2015

• tests and impl of GLs

  brentp

  committed
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Commits on Apr 1, 2015

• fix test

  brentp

  committed
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Commits on Mar 30, 2015

• add test for zero-division error from ESP. this closes #411 (fixed in previous commits).

  brentp

  committed
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Commits on Mar 26, 2015

• update test-pop to new testing format

  brentp

  committed
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Commits on Mar 24, 2015

• add tests

  brentp

  committed
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Commits on Mar 23, 2015

• add lots of tests for the (gts).(phenotype==2)... type queries

  brentp

  committed
  e77e821

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• short circuit some expensive ops

  brentp

  committed
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Commits on Mar 19, 2015

• fix de_novo debugging

  

  arq5x

  committed
  7a4fa29

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• Merge pull request #400 from brentp/annotate-vcf

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  arq5x

  committed
  45ce89e

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• add test to override column names and then select. cc @arq5x

  brentp

  committed
  39c6870

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• load multiple columns from VCF

  brentp

  committed
  6aa8e45

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• annotate with vcf:

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  brentp

  committed
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• annotate with vcf INFO field

  brentp

  committed
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• use compression funcs for all zlib/cPickle/npy stuff

  brentp

  committed
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Commits on Mar 18, 2015

• Merge pull request #394 from brentp/document-pre-processing

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  arq5x

  committed
  321c2cd

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• update exac test to match new vcf

  brentp

  committed
  08ac66e

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• update clinvar tests, prep, and parsing

  brentp

  committed
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Commits on Mar 17, 2015

• Change TPED test expected values to the variant_ids.

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  roryk

  committed
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• update cosmic test. note that we get duplicate ids because the id field can not be split by decompose

  brentp

  committed
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Commits on Mar 16, 2015

• add tests

  brentp

  committed
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Commits on Mar 8, 2015

• Provide a '--format sampledetail' option for showing denormalized sample output

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  chapmanb

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Commits on Mar 3, 2015

• correct --min-kindreds logic for compound heterozygotes.

  

  arq5x

  committed
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Commits on Mar 2, 2015

• add --min-kindreds to comp_hets and correct --only-affected behavior

  

  arq5x

  committed
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Commits on Feb 18, 2015

• add --families to auto_*, de_novo, and comp_hets

  

  arq5x

  committed
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• add --only-affected to de_novo tool

  

  arq5x

  committed
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Commits on Feb 9, 2015

• Order test results to match the new variant_sample ordering.

  roryk

  committed
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