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Commits on Nov 4, 2015
  1. @meganshand

    Addressing comments

    meganshand committed
Commits on Nov 3, 2015
  1. @meganshand
Commits on Nov 2, 2015
  1. @ldgauthier

    Merge pull request #1197 from broadinstitute/ts_ve_nullPointer

    ldgauthier committed
    Prevent null pointer exception in PrintMissingComp module
  2. @takutosato

    Removed the line that caused a null pointer, as the information it lo…

    takutosato committed
    …gged was not useful. Updated docs and added an integration test to ensure the code no longer throws the exception.
Commits on Oct 30, 2015
  1. @ldgauthier

    Merge pull request #1187 from broadinstitute/ldg_variantEval_famStrat

    ldgauthier committed
    Enable family-level stratification (if a ped file is provided)
Commits on Oct 28, 2015
  1. @ldgauthier
Commits on Oct 27, 2015
  1. @ldgauthier

    Merge pull request #1173 from broadinstitute/ldg_AS_annotations

    ldgauthier committed
    New map-combine-finalize annotation framework
  2. @fleharty

    Merge pull request #1190 from broadinstitute/mf_makeRDQHidden

    fleharty committed
    Fixed an NA12878 Knowledgebase test, and made the RDQ option for BQSR…
  3. @ldgauthier

    Finished draft of code for new map-combine-reduce annotation framework

    ldgauthier committed
    All VQSR annotations can be generated in allele-specific mode
    Pull out allele-specific annotations in AS_Standard annotation group
  4. @fleharty
  5. @ldgauthier

    Finished draft of code for new map-combine-reduce annotation framework

    ldgauthier committed
    All VQSR annotations can be generated in allele-specific mode
    Pull out allele-specific annotations in AS_Standard annotation group
Commits on Oct 26, 2015
  1. @ronlevine

    Merge pull request #1189 from broadinstitute/rhl_laatv_long_allele_choke

    ronlevine committed
    Allow LeftAlignAndTrimVariants to handle alleles longer than the default processing window
  2. @ronlevine
Commits on Oct 22, 2015
  1. @meganshand

    Merge pull request #1178 from broadinstitute/ms_ROCCurve

    meganshand committed
    ROCCurve High Confidence Mode
  2. @ronlevine

    Merge pull request #1182 from broadinstitute/rhl_laatv_multiallelic

    ronlevine committed
    Update doc for multiallelics, trimming is the default behavior
  3. @ronlevine
  4. @meganshand

    ROCCurve High Confidence Mode

    meganshand committed
    Integration Tests
    
    Updated test
    
    Changed method
    
    Minor changes
    
    Changed whitespace
    
    Fixed uncalled counts and 0 in R
    
    Fixed ReadBackedPileUp
    
    Removed imports and changed MD5
    
    Fixed failing test
    
    Adding vqslod color
    
    Updating script to create KB
    
    Fixing integration test now that the KB is bigger
    
    Adressing comments
Commits on Oct 14, 2015
  1. @takutosato
  2. @takutosato

    VariantAnnotator now supports annotating FILTER field from an externa…

    takutosato committed
    …l resource.
    
    Updated the docs.
Commits on Oct 12, 2015
  1. @ronlevine

    Merge pull request #1157 from broadinstitute/cn_sample_fix

    ronlevine committed
    Fix Sample mergeValues failure when merging identical string values
  2. @cmnbroad @ronlevine
Commits on Oct 9, 2015
  1. @ronlevine

    Merge pull request #1161 from broadinstitute/rhl_va_allele_match

    ronlevine committed
    VariantAnnotator checks alleles when annotating with external resource
Commits on Oct 8, 2015
  1. @ronlevine
  2. @ronlevine

    Merge pull request #1177 from broadinstitute/rhl_rev_1.140

    ronlevine committed
    Move htsjdk & picard to version 1.140
  3. @ronlevine
Commits on Oct 2, 2015
  1. @ldgauthier

    Merge pull request #1174 from broadinstitute/eb_fix_combine_for_spann…

    ldgauthier committed
    …ing_dels
    
    Fix for combining records in which one has a spanning deletion and ne…
  2. @eitanbanks

    Fix for combining records in which one has a spanning deletion and ne…

    eitanbanks committed
    …eds a padded reference allele.
    
    This was erroring out and not working.
Commits on Oct 1, 2015
  1. @vdauwera

    Merge pull request #1168 from broadinstitute/knoblett

    vdauwera committed
    Implemented MetricsCollection evaluation module
Commits on Sep 30, 2015
  1. @knoblett

    Implemented a new VariantEval evaulation module, MetricsCollection. F…

    knoblett committed
    …ixed null pointer exception, updated tests.
  2. @ronlevine

    Merge pull request #1167 from broadinstitute/rhl_bcbs

    ronlevine committed
    Implement BaseCounts per-sample
  3. @ronlevine
Commits on Sep 29, 2015
  1. @kshakir

    Merge pull request #1172 from broadinstitute/ks_jd_parallel_shell

    kshakir committed
    ParallelShell added as a new JobRunner
  2. @kshakir

    Minor updates to previous ParallelShell commit.

    kshakir committed
    Changed `--maximumNumberOfJobsToRunConcurrently`/`-maxConcurrentRun` to `Option[Int]`.
    Updated licenses.
    Added basic tests.
    Removed some IntelliJ warnings.
  3. @johandahlberg @kshakir

    ParallelShell added as a new JobRunner

    johandahlberg committed with kshakir
    The ParallelShell job runner will run jobs locally on one node concurrently as specified by the DAG, with the option to limit the maximum number of concurrently running jobs using the flag `maximumNumberOfJobsToRunConcurrently`.
    
    Signed-off-by: Khalid Shakir <kshakir@broadinstitute.org>
Commits on Sep 28, 2015
  1. @samuelklee

    Merge pull request #1165 from broadinstitute/sl_fix_no_calls

    samuelklee committed
    Changed calls for RGQ=0 from 0/0 to ./. in output of GenotypeGVCFs.
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