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Commits on Oct 30, 2013

• [BUG] all de novos in unaffected offspring

  

  arq5x

  committed
  f02b078

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• Merge branch 'master' of github.com:arq5x/gemini

  roryk

  committed
  8529d4a

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• Utility function to quote a string.

  roryk

  committed
  cce3dfa

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• Bug fix for missing attributes.

  roryk

  committed
  add7679

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• Bug fixes for JSON output, the unit test for amend

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  roryk

  committed
  a9e6790

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• Moved format selection to the GeminiQuery module.

  roryk

  committed
  86e612e

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• Added gemini amend.

  roryk

  committed
  b042c3c

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• Moved PED file parsing to the ped module.

  roryk

  committed
  7e8c2d6

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• Added a database_transaction context.

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  roryk

  committed
  935f137

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• Fixed error with JSON formatting.

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  roryk

  committed
  3981f40

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• Added gemini amend to edit an existing database.

  roryk

  committed
  8217d6c

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• Update Miniconda installer to latest version.

  chapmanb

  committed
  a7403f4

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Commits on Oct 28, 2013

• Added --nonsynonymous option to the C-alpha test.

  roryk

  committed
  5447023

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• Removed unused stub.

  roryk

  committed
  5c5d552

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Commits on Oct 25, 2013

• Merge branch 'master' of github.com:arq5x/gemini

  roryk

  committed
  6f147b8

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• Added --carrier-summary-by-phenotype.

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  roryk

  committed
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Commits on Oct 22, 2013

• [BUG] allow individual sample info from gt_* columns to be JSON serializable.

  

  arq5x

  committed
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Commits on Oct 16, 2013

• Remove --lsf-queue --torque-queue, etc options for loading.

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  roryk

  committed
  595282d

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• Handle snpEff/VEP specification checking in gemini_main via choices.

  roryk

  committed
  7ed2f30

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Commits on Oct 15, 2013

• Added SLURM support.

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  roryk

  committed
  439e9a6

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• 0.6.3a development in main

  chapmanb

  committed
  dd2c5e8

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• v0.6.2.2 point release to handle 0.6.2 install and test bugs

  chapmanb

  committed
  a6fc664

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• Ensure gemini can find configuration file relative to anaconda automated installation directory

  chapmanb

  committed
  a4e3bd7

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Commits on Oct 12, 2013

• Create the samples table from the existing schema during merge.

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  roryk

  committed
  970b161

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Commits on Oct 11, 2013

• Added --passonly flag to gemini load.

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  roryk

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Commits on Oct 10, 2013

• Added permutation testing.

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  arq5x

  authored and

  roryk

  committed
  ae34670

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Commits on Oct 9, 2013

• catch missing chrom exceptions for BigWig lookups

  

  arq5x

  committed
  b0f9873

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Commits on Oct 8, 2013

• bump to v0.6.2

  

  arq5x

  committed
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Commits on Oct 7, 2013

• add VEP format for version 73

  

  Uma Paila

  committed
  7bebc6a

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• Add a --devel flag to update allowing explicit retrieval of latest GitHub version

  chapmanb

  committed
  0ba53e7

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Commits on Oct 6, 2013

• fix merge goof

  

  arq5x

  committed
  978e09f

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• resolve conflicts

  

  arq5x

  committed
  592d61b

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• tweaks to auto_rec functionality for unaffected children

  

  arq5x

  committed
  db2ce02

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• [ENH] auto_* tools work without parents

  

  arq5x

  committed
  ae7cf78

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Commits on Oct 4, 2013

• Clarity edits, some docstrings added.

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  roryk

  committed
  e60ad11

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