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Commits on Mar 10, 2014

• dbnsfp annotation provenance

  

  arq5x

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Commits on Mar 3, 2014

• speedup loading for unit tests via --test-mode. Also provide --skip-gene-tables

  

  arq5x

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

  

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• don't index until end

  

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Commits on Feb 25, 2014

• Fix issue with missing __init__.py files that use namespace packages, which setuptools/pip toss away: update to latest ipython-cluster-helper with fix and manually patch for python-graph-core. Than…

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Commits on Feb 21, 2014

• Provide framework to make data files optional with switch to add new ones to avoid large downloads not used by default. Turn off gerp_bp download by default since it's 2/3 of the current download d…

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Commits on Feb 17, 2014

• Merge pull request #266 from dgaston/master

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• Added SPLICE_REGION to snpEff effects

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Commits on Feb 13, 2014

• Ensure mapping quality is a single value. Supports platypus VCF output

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Commits on Feb 11, 2014

• Avoid issues with numpy 1.7/1.8 discrepency in automated conda installation. Fixes #264

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Commits on Feb 8, 2014

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

  

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• merge in a transaction and delay indexing until final db.

  

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• better logging:

  

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• better logging:

  

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• add new indices

  

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Commits on Feb 5, 2014

• Merge pull request #262 from lbeltrame/add-samples-region

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Commits on Feb 4, 2014

• Add --show-samples to the output of gemini region

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• missing file

  

  arq5x

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• better parsing of PED files.

  

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• remove uncessary imports; refactor

  

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• parsers for new cancer tools

  

  arq5x

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• better support for the gene column

  

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• finalize the set_somatic tool

  

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Commits on Jan 21, 2014

• Merge pull request #256 from udp3f/master

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• update unit tests for stats tool

  

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• add num_hom_ref to stats tool under summarize

  

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• Merge pull request #255 from udp3f/master

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• minor

  

  udp3f

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• make naming consistent

  

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• add index

  

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• add docs for querying gene tables

  

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• add gene tables to database schema

  

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Commits on Jan 20, 2014

• Merge pull request #254 from udp3f/master

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• unit test for gene tables, loading with multiple cores

  

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• load with multiple cores: test gene table

  

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