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Commits on Nov 9, 2017
Commits on Oct 24, 2017
  1. Serialized GMM no longer depends on command line annotation order (#1…

    lucidtronix committed Oct 24, 2017
    …632)
    
    Order annotations by the order in the model report.
Commits on Sep 30, 2017
  1. Upgrade GKL to 0.6.0 (#1631)

    erniebrau authored and vdauwera committed Sep 30, 2017
Commits on Sep 6, 2017
  1. Update GKL to 0.5.9 (#1629)

    erniebrau authored and vdauwera committed Sep 6, 2017
Commits on Aug 29, 2017
  1. Revert "Changed GKL version to 0.5.6 (#1626)" (#1628)

    vdauwera committed Aug 29, 2017
    This reverts commit 78acfb9.
  2. Changed GKL version to 0.5.6 (#1626)

    erniebrau authored and vdauwera committed Aug 29, 2017
Commits on Aug 19, 2017
  1. Change to GKL 0.5.5, which fixes a bug in FPGA 'private' mode (#1623)

    erniebrau authored and vdauwera committed Aug 19, 2017
    Update GKL to version 0.5.5, which fixes a bug in FPGA 'private' mode. Integration test results were updated to reflect different fallback behavior when AVX is not available.
Commits on Aug 7, 2017
  1. Merge pull request #1622 from broadinstitute/rhl_vtt_fix_doc_typos

    vdauwera committed Aug 7, 2017
    Fix VariantsToTable documentation typos
  2. Merge pull request #1625 from broadinstitute/ldg_fixPLsubsettingGQpro…

    vdauwera committed Aug 7, 2017
    …blem
    
    Update the GQ after PLs get subset
Commits on Aug 4, 2017
Commits on Jul 29, 2017
Commits on Jul 28, 2017
  1. Merge pull request #1621 from broadinstitute/gvda_clean_slate

    vdauwera committed Jul 28, 2017
    Clean slate for the 3.8 release
  2. Update release scripts

    vdauwera committed Jul 28, 2017
  3. Updated gatkdocs template

    vdauwera committed Jul 28, 2017
  4. Fix problem filename

    vdauwera committed Jul 28, 2017
Commits on Jul 24, 2017
  1. Merge pull request #1615 from broadinstitute/gvda_archive_docs

    vdauwera committed Jul 24, 2017
    Archive GATK3-specific docs from the forum
Commits on Jul 23, 2017
  1. Merge pull request #1609 from broadinstitute/yf_make_readutils_test_p…

    vdauwera committed Jul 23, 2017
    …ublic
    
    making a test within readutils-test public
Commits on Jul 21, 2017
Commits on Jul 18, 2017
  1. Merge pull request #1610 from broadinstitute/ldg_fixRankSumHistogramO…

    ldgauthier committed Jul 18, 2017
    …utput2
    
    Changed ASRankSum single-sample output so it's combine-able
  2. Changed ASRankSum single-sample output so it's combine-able

    ldgauthier committed Jul 14, 2017
    single sample gVCF now gets a "histogram" with one entry
Commits on Jun 30, 2017
  1. Merge pull request #1608 from broadinstitute/ldg_renomalizeVQSRdata

    ldgauthier committed Jun 30, 2017
    Normalize input data by same annotation normalization scheme as input…
Commits on Jun 28, 2017
  1. Deprecate --allowMissingData, add --errorIfMissingData and print NA f…

    ronlevine committed Jun 26, 2017
    …or null object in VariantsToTable
Commits on Jun 27, 2017
  1. Merge pull request #1605 from broadinstitute/ldg_updateReference

    ldgauthier committed Jun 27, 2017
    Update all the md5s for header reference path changes
Commits on Jun 26, 2017
  1. Merge pull request #1604 from broadinstitute/rhl_close_printstream_1600

    ldgauthier committed Jun 26, 2017
    Close BQSRGatherer's PrintStream when finished