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Commits on May 18, 2016
Commits on Apr 28, 2016
Commits on Apr 4, 2016
Commits on Apr 3, 2016
  1. Updated BOSC bcbio/CWL abstract

    chapmanb committed Apr 3, 2016
    Incorporates comments from @ohofmann @tetron and @sjhosui
Commits on Apr 1, 2016
Commits on Mar 23, 2016
Commits on Feb 16, 2016
Commits on Feb 9, 2016
  1. HLA/hg38 status update

    chapmanb committed Feb 9, 2016
Commits on Jan 11, 2016
Commits on Jan 8, 2016
  1. Generalize SV circos-style plots with multi depth

    chapmanb committed Jan 8, 2016
    Cleans up logic for parsing and preparing based on depth. Removes
    -V sort parameter (fixes #107). Thanks to @brainstorm for suggestions.
Commits on Dec 18, 2015
Commits on Dec 14, 2015
  1. Merge pull request #106 from cmclean/master

    chapmanb committed Dec 14, 2015
    Explicitly added LICENSE file to bcbio-gff.
Commits on Dec 11, 2015
Commits on Nov 29, 2015
  1. Merge pull request #104 from mspinelli/master

    chapmanb committed Nov 29, 2015
    Added inferred strand for inferred parent when safe
Commits on Nov 23, 2015
  1. Last commit accidently changed the assert

    mspinelli committed Nov 23, 2015
    Reverted back to what it was from the latest pull (I was working originally on an older version of the code when the assert was ==0 not > 0.
  2. Added Inferred stand when adding inferred parent

    mspinelli committed Nov 23, 2015
    If all the children sequences are on the same strand, then instead of making the inferred strand "None", make it match the children strands.
Commits on Nov 18, 2015
Commits on Nov 17, 2015
  1. CSHL teaching slides

    chapmanb committed Nov 17, 2015
    - Update with HLA details plus improvements to graph genotyping.
    - Finalize to match teaching materials and example AMI with
      run information.
Commits on Nov 12, 2015
Commits on Nov 9, 2015
Commits on Nov 5, 2015
Commits on Nov 2, 2015
  1. Merge pull request #103 from hredestig/master

    chapmanb committed Nov 2, 2015
    make python 3 compatible
Commits on Oct 28, 2015
  1. make python 3 compatible

    Henning Redestig committed Oct 28, 2015
    next(x) works in both 3 and 2 but x.next() only works in 2
Commits on Sep 23, 2015
Commits on Sep 11, 2015
  1. hg38 validation post improvements

    chapmanb committed Sep 11, 2015
    - Update plots with consistent axes and coloring to distinguish SNP
      and indel comparisons. Thanks to @ohofmann
    - Update text about FreeBayes discordants after digging into issues.
    - Fix typos, thanks to @mjafin
Commits on Sep 8, 2015
  1. hg38 validation with better plotting

    chapmanb committed Sep 8, 2015
    Move to FNR and FDR plots for variant validations and update post
    with new details.
Commits on Sep 3, 2015
  1. Improve hg38 validation post

    chapmanb committed Sep 3, 2015
    - Fixes comparisons to consistently use hard filtering and improve
      default GATK MQ filters. Update text to reflect less confusing
      comparisons.
    - Clarify text in many locations thanks to comments from @ohofmann
    - Include details about pre-processing thanks to @dakl
Commits on Sep 1, 2015
  1. Move hg38 validation post to markdown to avoid missing links. Fixes t…

    chapmanb committed Sep 1, 2015
    …o text based on helpful comments from @deannachurch.
Commits on Aug 31, 2015
Commits on Jul 12, 2015
  1. Notes from BOSC 2015 day 2

    chapmanb committed Jul 12, 2015
Commits on Jul 11, 2015