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Commits on Sep 23, 2015

• bump to 0.17.1

  

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Commits on Sep 22, 2015

• populate eval dict with sample_info. Thanks @udp3f for reporting.

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Commits on Sep 18, 2015

• give max_aaf_all a real type.

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Commits on Sep 15, 2015

• clarify that --gt-pl-max is per family.

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• clarify docs about -d option being per-family

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• Fix distributed loading of VEP with extra columns

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Commits on Sep 8, 2015

• fix for extra error messages reported by Bianca.

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Commits on Sep 7, 2015

• missing file

  

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Commits on Sep 3, 2015

• only show confident comp hets by default adjust with --max-priority

  brentp

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• remove all vestiges of --no-bcolz

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• Merge branch 'arq5x_master' into no_default_bcolz

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Commits on Sep 1, 2015

• by default, we dont load the info field.

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Commits on Aug 29, 2015

• Merge pull request #540 from brentp/genewise

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Commits on Aug 28, 2015

• don't create bcolz index by default.

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Commits on Aug 23, 2015

• Update to IPython 4.0

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• Additional handling of inputs missing ALT alleles

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Commits on Aug 22, 2015

• Handle no alts in allele-based annotation loading

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Commits on Aug 21, 2015

• document gene_wise tool

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• rename columns and sanity-check input

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• re-order and fix column naming

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• + output the number of filters that passed per-variant.

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Commits on Aug 20, 2015

• output per-gene and per-variant passes

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• Merge pull request #537 from brentp/max_aaf_all_fix

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• fix max_aaf_all calculation using coalesce. previously, if any

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• Avoid use of tempdir for chunks when using IPython

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• fix case where 'gene' is not specified in requested columns.

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• new genewise tool. see #529

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Commits on Aug 19, 2015

• Merge branch 'arq5x_master' into aaf_all_max

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• use --families to limit queries *before* any work is done.

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• add max_aaf_all column.

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• Merge pull request #532 from brentp/cyvcf2

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Commits on Aug 18, 2015

• update requirements, remove vestiges of previous loading mechanism

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• final fixes for cyvcf2

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Commits on Aug 17, 2015

• update to cyvcf2.

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• dont double-print message

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