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Commits on May 15, 2015
  1. @vdauwera
  2. @vdauwera
  3. @vdauwera

    Merge pull request #979 from broadinstitute/ami-fixASE-bug

    vdauwera authored
    solve bug - now work also when the reads does not have mate
  4. @vdauwera

    Merge pull request #978 from broadinstitute/dr_rev_htsjdk_and_picard

    vdauwera authored
    Rev htsjdk to version 1.132 and picard to version 1.131, and switch to using the versions in maven central
Commits on May 14, 2015
  1. @droazen

    Rev htsjdk to version 1.132 and picard to version 1.131, and switch t…

    droazen authored
    …o using the versions in maven central
    
    -We now pull htsjdk and picard from maven central.
    
    -Updated the GATK codebase as necessary to adapt to changes in the Feature
     interface.
    
    -Since VCFHeader now requires that all header lines have unique keys, uniquified
     the keys of GVCFBlock header lines by including the min/max GQ in the key.
     Updated MD5s accordingly.
    
    -Other MD5s changed as a result of an htsjdk fix to eliminate "-0" in VCF output.
Commits on May 13, 2015
  1. @vdauwera

    Merge pull request #947 from broadinstitute/rhl_invert_selection

    vdauwera authored
    Added --invert_selection flag for variant selection queries
  2. @eitanbanks

    Merge pull request #981 from broadinstitute/eb_no_lone_dels

    eitanbanks authored
    Fixed a small feature/bug that I introduced with the spanning deletions genotyping
  3. @eitanbanks

    Fixed a small feature/bug that I introduced with the spanning deletio…

    eitanbanks authored
    …ns genotyping.
    
    In the case where there's a low quality SNP under a spanning deletion in the gvcfs:
    if the SNP is not genotyped by GenotypeGVCFs (because it's just noise) we were still
    emitting a record with just the symbolic DEL allele (because that allele is high quality).
    
    We no longer do that.
Commits on May 12, 2015
  1. @amilev

    solve bug - now work also when the reads does not have mate

    amilev authored
    reads with no mate will be counted as valid reads
  2. @ronlevine
  3. @vdauwera

    Merge pull request #974 from broadinstitute/jw_Var2BinPEDSwap

    vdauwera authored
    Correct errant array element swap in FAM file output.
  4. @eitanbanks

    Merge pull request #938 from broadinstitute/eb_fix_spanning_deletions…

    eitanbanks authored
    …_in_genotyping
    
    Added a fix for genotyping positions over spanning deletions.
  5. @whitejo

    Correct errant array element swap in FAM file output.

    whitejo authored
    dad and mom are swapped; paternal first, then maternal
    
    updated MD5 chksums for test files
    
    remove commented lines
Commits on May 11, 2015
  1. @eitanbanks

    Added a fix for combining/genotyping positions over spanning deletions.

    eitanbanks authored
    Previously, if a SNP occurred in sample A at a position that was in the middle of a deletion for sample B,
    sample B would be genotyped as homozygous reference there (but it's NOT reference - there's a deletion).
    Now, sample B is genotyped as having a symbolic DEL allele.
    
    Minor cleanup added.  Note that I also removed Laura's previous fix for this problem.
    
    Existing integration tests change because I've added a new header line to the VCF being output.
    I also added several tests for the new functionality showing:
    1. genotyping from separate and already combined gvcfs give the same output
    2. genotyping over multiple spanning deletions works
    3. combining works too
    
    Existing unit tests also cover this case.
  2. @vdauwera

    Merge pull request #948 from broadinstitute/jw_deprecate_merge_var

    vdauwera authored
    Jw deprecate mergeVariantsViaLD argument
Commits on May 8, 2015
  1. @whitejo @vdauwera

    Deprecate --mergeVariantsViaLD in HC

    whitejo authored vdauwera committed
    New unit test for deprecated mergeVariantsViaLD
    Update HaplotypeCallerIntegrationTest.java
    Delete duplicate testHaplotypeCallerMergeVariantsViaLDException test.
Commits on May 3, 2015
  1. @vdauwera

    Merge pull request #968 from broadinstitute/gg_unexclude_annotations_…

    vdauwera authored
    …#966
    
    Un-exclude SD and TRA from HC annotators
Commits on May 2, 2015
  1. @vdauwera
  2. @vdauwera

    Un-exclude SD and TRA from HC annotators; resolves #966

    vdauwera authored
    Exclude MQ0BySample
    Move SD and TRA to new StandardUGAnnotation interface
    There is now annotation interface (StandardUGAnnotation) holding annots that are standard in UG but should't be used as they are now with HC. This allows us to not have to exclude these annotations explicitly in HC, but still be able to use them for development purposes.
  3. @vdauwera

    Merge pull request #970 from broadinstitute/gg_minor_docfixes

    vdauwera authored
    Fairly minor if plentiful fixes to various gatkdocs. Merging this without formal review since all tests pass, the gatkdocs build, and no one really wants to review corrections to grammar, typos and layout for 120+ documents. Review will be done by users in production ;-)
  4. @vdauwera
Commits on May 1, 2015
  1. @vdauwera

    Merge pull request #965 from broadinstitute/gg_nsubtil_clamp_hmm_fix

    vdauwera authored
    Clamp the HMM window starting coordinate to 1 instead of 0
Commits on Apr 30, 2015
  1. @ldgauthier

    Merge pull request #967 from broadinstitute/rhl_va_allele_trim

    ldgauthier authored
    More allele trimming for VariantAnnotator
  2. @ronlevine
Commits on Apr 29, 2015
  1. @vdauwera
Commits on Apr 28, 2015
  1. @droazen

    Merge pull request #952 from broadinstitute/dr_queue_qsub_broad

    droazen authored
    Queue: add -qsub-broad argument
Commits on Apr 27, 2015
  1. @droazen

    Queue: add -qsub-broad argument

    droazen authored
    When -qsub-broad is specified instead of -qsub, use the "h_vmem" parameter
    instead of "h_rss" to specify memory limit requests.
    
    Also cause the GridEngine native arguments to be output by default to the logger,
    instead of only when in debug mode.
  2. @vdauwera

    Merge pull request #943 from broadinstitute/ldg_fixAllowNonUniqueKmers

    vdauwera authored
    Fix implementation of allowNonUniqueKmersInRef so that it applies to all...
Commits on Apr 23, 2015
  1. @ldgauthier
Commits on Apr 21, 2015
  1. @eitanbanks

    Merge pull request #930 from broadinstitute/rhl_bad_edge_pileup

    eitanbanks authored
    Bypass edge alignment reads while making pileup
  2. @ronlevine
Commits on Apr 16, 2015
  1. @vdauwera

    Merge pull request #932 from broadinstitute/yf_fix_picard_md

    vdauwera authored
    Fix the scala wrapper for Picard MarkDuplicates
Commits on Apr 15, 2015
  1. @kshakir

    Merge pull request #934 from broadinstitute/ks_cat_variants_extensions

    kshakir authored
    CatVariants now allows different input / output file types.
Commits on Apr 13, 2015
  1. @kshakir

    CatVariants now allows different input / output file types.

    kshakir authored
    Escaping the CatVariantsIntegrationTest classpaths for possible spaces in the directory names.
  2. @yfarjoun

    since Picard mark duplicates moved to a different package, this class…

    yfarjoun authored
    … was broken. here's the fix. it would be good to have tests for all the scala picard-wrappers, but that is out of scope for this commit.
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