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Commits on Oct 24, 2014
  1. @vdauwera
  2. @vdauwera
Commits on Oct 23, 2014
  1. @vdauwera

    Merge pull request #761 from broadinstitute/ks_junction_plugin_local_…

    vdauwera authored
    …repo
    
    Adding sysinternals:junction:1.04:exe to local repo.
  2. @kshakir

    Adding sysinternals:junction:1.04:exe to local repo.

    kshakir authored
    With Geraldine's blessing, works around issue where the repo for this exe keeps going down.
  3. @droazen
  4. @kshakir

    Queue patches.

    kshakir authored
    Fixed Queue bug with bad localhost addresses.
    Spaces in job names, while fine in GridEngine 6, break in (Son of) GE8.
  5. @vdauwera

    Merge pull request #759 from broadinstitute/gg_minor_docfixes

    vdauwera authored
    Minor documentation clarifications in HC and a typo fix in SelectVariants
Commits on Oct 22, 2014
  1. @vdauwera
  2. @rpoplin

    Merge pull request #755 from broadinstitute/sc_Annotation_Docs_73647570

    rpoplin authored
    Improvements to documentation of variant annotations
  3. @rpoplin

    Merge pull request #740 from broadinstitute/rp_ROC_curve_total_sensit…

    rpoplin authored
    …ivity
    
    Adding total sensitivity option to ROCCurveNA12878 to help with Mauricio...
  4. @rpoplin
  5. @kshakir

    Merge pull request #757 from broadinstitute/ks_smowton_scatter_contig…

    kshakir authored
    …s_fix
    
    Improved scatter contigs algorithm to be fairer when splitting many contigs into few parts.
  6. @kshakir

    Minor fixups for previous commit once tests (only runnable at Broad) …

    kshakir authored
    …were run.
    
    Fixed off by one error in size calculation IntervalUtils.scatterContigIntervals().
    In test for fewer files than intervals, adjusted expected intervals.
    In test for more files than intervals, adjusted expected exception.
  7. @smowton @kshakir

    Improved scatter contigs algorithm to be fairer when splitting a larg…

    smowton authored kshakir committed
    …e number of contigs into a small number of parts.
    
    See also: http://gatkforums.broadinstitute.org/discussion/comment/16010
    
    Signed-off-by: Khalid Shakir <kshakir@broadinstitute.org>
Commits on Oct 21, 2014
  1. @chandrans @vdauwera

    Improvements to documentation of variant annotations

    chandrans authored vdauwera committed
    	- Added or modified explanations for majority of variant annotations
    	- Generalized NBaseCount to include all tech platforms (not just SOLiD)
  2. @vdauwera
  3. @droazen

    Merge pull request #743 from broadinstitute/gg_gsaweb_switchover

    droazen authored
    Switch GATKDocs publishing to new gsaweb VM
  4. @rpoplin

    Merge pull request #754 from broadinstitute/rhl_variant_array_exception

    rpoplin authored
    Do not process a variant if it is too large (> readLength), and log an e...
  5. @rpoplin

    Merge pull request #753 from broadinstitute/ldg_HCzeroDepth

    rpoplin authored
    Fix GenotypeGVCF bugs in -allSites mode
  6. @rpoplin

    Merge pull request #752 from broadinstitute/pd_cran_license

    rpoplin authored
    Changed license of gsalib R package from BSD to MIT
  7. @rpoplin

    Merge pull request #751 from broadinstitute/pd_bamout_ref_regions

    rpoplin authored
    Added -disableOptimizations argument to HaplotypeCaller.
  8. @ldgauthier

    Variants that become hom-ref after regenotyping in GenotypeGVCFs are …

    ldgauthier authored
    …now getting output in -allSites mode.
  9. @ldgauthier
Commits on Oct 20, 2014
  1. Do not process a variant if it is too large (> readLength), and log a…

    Ron Levine authored
    …n error
    
    remove final keyword before refMap and altMap, constructHaplotype() changes their values
    
    return ArtificialHaplotype from constructHaplotype instaed of passing as an argument
    
    Add logic so arraycopy does not throw an IndexOutOfBoundsException, add test for a long insert
Commits on Oct 17, 2014
  1. @pdexheimer
  2. @pdexheimer

    Added -disableOptimizations argument to HaplotypeCaller.

    pdexheimer authored
      * This argument is intended to be used in conjunction with -bamout, and disable early-exit optimizations to allow reference regions to be contained in the output bam
      * Also forcibly includes the reference haplotype in the set of haplotypes given to the BAMWriter
      * Made -dontTrimActiveRegions visible, as it is likely also desirable in this use case
      * Addresses PT 77731660
Commits on Oct 16, 2014
  1. @ldgauthier

    Merge pull request #750 from broadinstitute/ldg_uniqueSamplesInCombin…

    ldgauthier authored
    …eVariants
    
    Throw UserException if input VCFs have duplicate samples but no genotype...
Commits on Oct 15, 2014
  1. @ldgauthier

    Throw UserException if input VCFs have duplicate samples but no genot…

    ldgauthier authored
    …ypemergeoption is specified
  2. @rpoplin

    Merge pull request #749 from broadinstitute/ldg_CGPfasterTests

    rpoplin authored
    Decrease interval on CGP integration test to reduce test execution time
  3. @rpoplin

    Adding total sensitivity option to ROCCurveNA12878 to help with Mauri…

    rpoplin authored
    …cio's analyses.
    
    -- We now keep a tally of uncalled sites so that they can be factored into the denominator of the sensitivity/specificity metric
  4. @ldgauthier
  5. @rpoplin

    Merge pull request #747 from broadinstitute/gg_fixLicenseOmission

    rpoplin authored
    Updated license files and text
Commits on Oct 14, 2014
  1. @vdauwera

    Updated license information

    vdauwera authored
    - Updated license files (private/protected) for version, address and a couple of legal clauses
    - Updated license snippet throught the codebase
  2. @rpoplin

    Merge pull request #748 from broadinstitute/rp_roc_curve_qual_field

    rpoplin authored
    In ROCCurveNA12878, if VQSLOD value is not present default to using the ...
  3. @rpoplin

    In ROCCurveNA12878, if VQSLOD value is not present default to using t…

    rpoplin authored
    …he QUAL field instead to rank the variants.
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