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Commits on Jun 1, 2016
  1. Merge pull request #1394 from broadinstitute/gvda_add_colt_dependency

    Add colt > cern.jet.normal dependency
    vdauwera committed Jun 1, 2016
  2. Merge pull request #1391 from broadinstitute/rhl_htsjdk_picard_2.4.1

    Move htsjdk and picard to version 2.4.1
    vdauwera committed Jun 1, 2016
  3. Merge pull request #1392 from broadinstitute/gvda_vqsr_retries_mdp

    Ability to retry building VQSR model (contributed by mdp)
    vdauwera committed Jun 1, 2016
Commits on May 31, 2016
Commits on May 29, 2016
  1. GATKDocs overhaul

        - Fixed displaying of default values
        - Removed code cruft
        - Reorganized tooldoc categories and improved names
        - Reorganized tools within categories where applicable
        - Touched up various tool docs
        - Switched default gatkdocs output to html
        - Added parameter in agrregator pom to control output type
        - Set gatkdocs publishing script to output php
        - Deprecated GenotypeAndValidate walker
        - Added back PhoneHome arguments with @Deprecated annotations
    vdauwera committed May 27, 2016
Commits on May 27, 2016
  1. Remove Phone Home

    vdauwera committed May 27, 2016
  2. Merge pull request #1374 from broadinstitute/gvda_move_ReassignOrigin…

    …alMQAfterIndelRealignment_toPublic_#1364
    
    Code cleanup campaign pre-3.6; see itemized commit messages.
    vdauwera committed May 27, 2016
  3. Merge pull request #1377 from broadinstitute/vrr_non_ref_likelihood_r…

    …ecal
    
    Fix for the sum(AD) > DP bug.
    vruano committed May 27, 2016
Commits on May 26, 2016
  1. Fix for the sum(AD) > DP bug.

    Closes issue #1340
    vruano committed Apr 25, 2016
  2. Added option to validate gvcf (for ValidateVariants) (#1379)

    * with option --gvcf CLP will now put extra checks that a gvcf must adhere to (existance of <NON_REF> allele at every variant, and that the variants in total cover the entire requested intervals, or the whole genome if no intervals have been specified)
    * works on gvcf produced by HC when using either GVCF or BP_RESOLUTION mode
    * added positive and negative tests
    yfarjoun committed May 26, 2016
Commits on May 25, 2016
  1. Fix error in InfiniteRandomMatingPopulationModel.getLikelihoodsCalcul…

    …ator
    
    Same issue noticed in GATK4 [here](broadinstitute/gatk#1856)
    SHuang-Broad committed May 25, 2016
Commits on May 19, 2016
  1. Merge pull request #1375 from broadinstitute/gvda_fix_offbyone_maxAlt…

    …Alls_M2_#1297
    
    Fixed M2 max alt alleles threshold evaluation error
    vdauwera committed May 19, 2016
  2. Merge pull request #1358 from broadinstitute/sl_issue_1327

    Changed calls with GQ=0 to no-call for HaplotypeCaller in normal mode.
    samuelklee committed May 19, 2016
  3. Merge pull request #1370 from broadinstitute/ldg_fixBQresMQ

    Add fix and test for finalizing MQ annotation at BP resolution for va…
    ldgauthier committed May 19, 2016
  4. Add fix and test for finalizing MQ annotation at BP resolution for va…

    …riant and ref samples
    
    Addresses issue #1356
    ldgauthier committed May 4, 2016
  5. Fixed M2 max alt alleles threshold evaluation error

        Also clarified some argument docs
    vdauwera committed May 18, 2016
Commits on May 18, 2016
  1. Merge pull request #1352 from broadinstitute/mf_othersrequired

    Adds othersRequired so that some arguments can require other arguments in order to work.
    fleharty committed May 18, 2016
Commits on May 17, 2016
  1. Adding OtherArgumentRequired option to allow an argument to require a…

    …n additional argument.
    fleharty committed Apr 22, 2016
  2. Merge pull request #1372 from broadinstitute/gvda_docfix_CV_syntax

    Fix VCF tagging syntax in CombineVariants doc
    vdauwera committed May 17, 2016
  3. Fix tagging syntax

    Syntax was given as -V:format,name but should be -V:name,format
    vdauwera committed May 17, 2016
  4. Merge pull request #1371 from broadinstitute/rhl_htsjdk_picard_2.2.2

    Move htsjdk and picard to version 2.3.0
    ronlevine committed May 17, 2016
Commits on May 16, 2016