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Commits on Jun 1, 2016
  1. @vdauwera
  2. @vdauwera
  3. @vdauwera

    Merge pull request #1394 from broadinstitute/gvda_add_colt_dependency

    Add colt > cern.jet.normal dependency
    vdauwera committed Jun 1, 2016
  4. @vdauwera
  5. @vdauwera

    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
  6. @ronlevine
  7. @vdauwera

    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
  1. @vdauwera
  2. @vdauwera
Commits on May 29, 2016
  1. @vdauwera

    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. @vdauwera
  2. @vdauwera

    Remove Phone Home

    vdauwera committed May 27, 2016
  3. @vdauwera

    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
  4. @vdauwera
  5. @vdauwera
  6. @vdauwera
  7. @vdauwera
  8. @vdauwera
  9. @vdauwera
  10. @vruano

    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. @vruano

    Fix for the sum(AD) > DP bug.

    Closes issue #1340
    vruano committed Apr 25, 2016
  2. @yfarjoun

    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. @SHuang-Broad

    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. @vdauwera

    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. @samuelklee

    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. @ldgauthier

    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. @ldgauthier

    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. @vdauwera

    Fixed M2 max alt alleles threshold evaluation error

        Also clarified some argument docs
    vdauwera committed May 18, 2016
Commits on May 18, 2016
  1. @fleharty

    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
  2. @samuelklee
Commits on May 17, 2016
  1. @fleharty

    Adding OtherArgumentRequired option to allow an argument to require a…

    …n additional argument.
    fleharty committed Apr 22, 2016
  2. @vdauwera

    Merge pull request #1372 from broadinstitute/gvda_docfix_CV_syntax

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

    Fix tagging syntax

    Syntax was given as -V:format,name but should be -V:name,format
    vdauwera committed May 17, 2016
  4. @ronlevine

    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
  1. @ronlevine