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Commits on Dec 12, 2016
Commits on Dec 10, 2016
  1. Merge pull request #1533 from broadinstitute/lb_update_jexl_behavior

    Rev htsjdk + update jexl behavior
    vdauwera committed on GitHub Dec 10, 2016
  2. Move htsjdk to ver 2.8.1 and picard to ver 2.7.2

         - Updating VF and tests to match new jexl behavior from htsjdk
         - Use Z instead of DP to test behavior on missing annotation
    ronlevine committed with vdauwera Dec 7, 2016
Commits on Dec 6, 2016
  1. Merge pull request #1529 from broadinstitute/ms_fs

    Make Fisher Exact Test match R and GATK4 p-values
    meganshand committed on GitHub Dec 6, 2016
  2. Merge pull request #1528 from broadinstitute/rhl_validate_vcf.gz

    Output filenames with the vcf.gz extension are gzipped, those containing the string ".bcf" result in VCF
    ronlevine committed on GitHub Dec 6, 2016
  3. Output files with the vcf.gz extension are gzipped, containing .bcf n…

    …ot as an extension result in VCF"
    ronlevine committed Dec 2, 2016
  4. Merge pull request #1496 from broadinstitute/db_m2_downsampling

    Expose downsampling parameters as CLI arguments to Mutect2
    vdauwera committed on GitHub Dec 6, 2016
Commits on Dec 5, 2016
  1. Merge pull request #1520 from broadinstitute/gvda_more_docfixes_for_3.7

    Documentation fixes
    vdauwera committed on GitHub Dec 5, 2016
  2. Add downsampling arguments to Mutect

    	- maxReadsInRegionPErSample, minReadsPerAlignment start are now M2 args
    	- maxReadsInMemoryPerSample is an activeRegionWalker arg
    davidbenjamin committed with vdauwera Oct 19, 2016
  3. Documentation fixes

    	- Fix missing closing code block tag
    	- SOR fix + minor fix to template
    	- Minor typo fixes
    	- Make no_cmdline_in_header arg visible in docs
    	- Caveats for UG-only args that are difficult to move out of common collection
    	- Reference -L and -XL in -gvcf documentation
    	- Annotation doc fixes (dsde-docs#1289)
    	- Unhide some ContEst args and make Advanced
    	- Fix inputPrior error message
    	- Update web urls
    	- Add JEXL doc link
    vdauwera committed Jun 4, 2016
Commits on Nov 30, 2016
  1. Merge pull request #1527 from broadinstitute/rhl_vc_writer_factory_to…

    …_builder
    
    Replace VariantContextWriterFactory with VariantContextWriterBuilder
    ronlevine committed on GitHub Nov 30, 2016
Commits on Nov 23, 2016
  1. Merge pull request #1522 from broadinstitute/rhl_sam_error_1427

    Make exit system file type message generic
    ronlevine committed on GitHub Nov 23, 2016
Commits on Nov 18, 2016
  1. Merge pull request #1517 from broadinstitute/rhl_adapter_boundary_err…

    …_1406
    
    Fix adapter bounday for positive strand
    davidbenjamin committed on GitHub Nov 18, 2016
Commits on Nov 16, 2016
  1. Merge pull request #1354 from broadinstitute/db_issue_1351

    Fixed logic error in AlleleBalance Annotation.  Closes #1351.
    ronlevine committed on GitHub Nov 16, 2016
Commits on Nov 15, 2016
  1. Merge pull request #1516 from broadinstitute/rhl_replace_test_file_1514

    Change the truth VCF
    ronlevine committed on GitHub Nov 15, 2016
  2. Change the truth VCF

    ronlevine committed Nov 15, 2016
  3. Merge pull request #1506 from broadinstitute/rhl_set_htsjdk_log_level

    Set HTSJDK log level
    ronlevine committed on GitHub Nov 15, 2016
  4. Set HTSJDK log level

    ronlevine committed Nov 8, 2016
Commits on Nov 14, 2016
  1. Merge pull request #1507 from broadinstitute/gvda_treereduce_vf_#1147

    Added TreeReduce interface to VariantFiltration
    ronlevine committed on GitHub Nov 14, 2016
  2. Merge pull request #1511 from broadinstitute/rhl_fix_stand_conf_for_c…

    …alling_1510
    
    Change default value of STANDARD_CONFIDENCE_FOR_CALLING to 10
    vdauwera committed on GitHub Nov 14, 2016
Commits on Nov 11, 2016
Commits on Nov 8, 2016
  1. Merge pull request #1494 from broadinstitute/rhl_bcs_pos_1493

    BaseCountsBySample counting bases at a particular position
    ronlevine committed on GitHub Nov 8, 2016
Commits on Nov 1, 2016
  1. Merge pull request #1502 from broadinstitute/db_port_qual_tweaking

    Backport numerics changes in new qual
    vruano committed on GitHub Nov 1, 2016
Commits on Oct 27, 2016
  1. fixed a max priority Q error while removing alt alleles when faced wi…

    …th high ploidy and allele count; added hackish integration test (#1457)
    SHuang-Broad committed on GitHub Oct 27, 2016
Commits on Oct 24, 2016
  1. Merge pull request #1498 from broadinstitute/rhl_warn_to_stderr_1497

    Write saved WARN messages to stderr instead of stdout
    vruano committed on GitHub Oct 24, 2016
Commits on Oct 21, 2016