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branch: master

Mar 18, 2014

  1. droazen

    Disable GATKRunReportUnitTest

    These tests pass individually and as part of complete test suite runs,
    but cause an intermittent NoSuchElementException in maven when the
    unit tests are run on their own. Disabling these tests until the
    cause of this can be identified.
    authored
  2. droazen

    Merge remote-tracking branch 'unstable/master'

    authored
  3. droazen

    Update pom versions for 3.1

    authored

Mar 17, 2014

  1. droazen

    Merge pull request #567 from broadinstitute/dr_public_GATKRunReport_t…

    …ests
    
    Move GATKRunReport tests from private to public
    authored
  2. droazen

    Move GATKRunReport tests from private to public

    -Hide AWS downloader credentials in a private properties file
    -Remove references to private ActiveRegion walker
    
    Allows phone home functionality to be tested at release time
    when we are running tests on the release jar.
    authored
  3. droazen

    Merge pull request #561 from broadinstitute/ks_package_classpath

    Updated package-tests classpath, and allowing javac -cp <package>.jar.
    authored
  4. Eric Banks

    Merge pull request #563 from broadinstitute/aw_refactor_tribble

    GATK changes to conform to Tribble refactoring as part improving Tabix s...
    authored
  5. Eric Banks

    Merge pull request #565 from broadinstitute/eb_remove_one_more_refere…

    …nce_to_rr
    
    Remove unused and unnecessary argument
    authored
  6. Eric Banks

    Remove unused and unnecessary argument

    authored
  7. Eric Banks

    Merge pull request #564 from broadinstitute/eb_rename_truth_set

    Mark had mis-named this input callset to the knowledgebase.  It's the pi...
    authored
  8. Eric Banks

    Mark had mis-named this input callset to the knowledgebase. It's the …

    …pilot2 liftover, not pilot1.
    authored
  9. alecw

    GATK changes to conform to Tribble refactoring as part improving Tabi…

    …x support in Tribble (among other things).
    
    1. Enable on-the-fly indexing for vcf.gz.
    2. Handle on-the-fly indexing where file to be indexed is not a regular file, thus index should not be created.
    3. Add method setProgressLogger to all SAMFileWriter implementations.
    4. Revved picard to 1.109.1722
    5. IndelRealigner md5s change because the MC tag is added to records now.
    
    Fixed up and signed off by ebanks.
    authored eitanbanks committed
  10. Eric Banks

    Merge pull request #554 from broadinstitute/bh_SOR_new_annotation

    Bh sor new annotation
    authored
  11. Eric Banks

    Merge pull request #562 from broadinstitute/ldg_newCGPdocs

    Added documentation category for CalculateGenotypePosteriors
    authored
  12. ldgauthier

    Added documentation category for CalculateGenotypePosteriors

    authored
  13. Ryan Poplin

    Merge pull request #559 from broadinstitute/vrr_assembly_graph_edge_i…

    …nfo_revise
    
    Improved criteria to select best haplotypes out from the assembly graph.
    authored
  14. kshakir

    Updated package-tests classpath, and allowing javac -cp <package>.jar.

    Package tests now hard coding just the gatk-framework tests jar, to include ONLY BaseTest, until the exclusions may be debugged.
    Removing cofoja's annotation service from the package jars, to allow javac -cp <package>.jar.
    authored

Mar 14, 2014

  1. Valentin Ruano Rubio

    Improved criteria to select best haplotypes out from the assembly graph.

    Currently the best haplotypes are those that accumulate the largest ABSOLUTE edge *multiplicity* sum across their path in the assembly graph.
    
    The edge *mulitplicity* is equal to the number of reads that expand through that edge, i.e. have a kmer that uniquely map to some vertex up-stream from the edge and the following base calls extend across that edge to vertices downstream from it.
    
    Despite that it is obvious that higher multiplicties correlated with haplotype probability this criterion fails short in some regards of which the most relevant is:
    
    As it is evaluated in condensed seq-graph (as supposed to uncompressed read-threading-graphs) it is bias to haplotypes that have more short-sequence vetices
      ( -> ATGC -> CA -> has worse score than -> A -> T -> G -> C -> C -> A ->). This is partly result of how we modify the edge multiplicities when we merge vertices from a linear chain.
    
    This pull-request addresses the problem by changing to a new scoring schema based in likelihood estimates:
    
    Each haplotype's likelihood can be calculated as the multiplication of the likelihood of "taking" its edges in the assembly graph. The likelihood of "taking" an edge in the assembly
    graph is calculated as its multiplicity divide by the sum of multiplicity of edges that share the same source vertex.
    
    This pull-request addresses the following stories:
    
    https://www.pivotaltracker.com/story/show/66691418
    https://www.pivotaltracker.com/story/show/64319760
    
    Change Summary:
    
    1. Change to the new scoring schema.
    2. Added a graph DOT printing code to KBestHaplotypeFinder in order to diagnose scoring.
    3. Graph transformation have been modified in order to generate no 0-multiplicity edges. (Nevertheless the schema above should work with 0 edges assuming that they are in fact 0.5)
    authored
  2. Bertrand

    New abstract class StrandBiasTest() with old sub-class FisherStrand()…

    … and new sub-class StrandOddsRatio(). Latter is test based on symmetric odds ratio more appropriate than Fisher exact test when number of samples is large.
    
    https://www.pivotaltracker.com/story/show/66087886
    authored
  3. Eric Banks

    Merge pull request #560 from broadinstitute/dr_fix_phone_home_packagi…

    …ng_error
    
    Unconditionally include all of commons-httpclient in the GATK/Queue jars
    authored
  4. droazen

    Unconditionally include all of commons-httpclient in the GATK/Queue jars

    The maven shade plugin was eliminating a necessary class (IgnoreCookiesSpec)
    when packaging the GATK/Queue. Work around this by telling maven to
    always package all of commons-httpclient.
    authored

Mar 12, 2014

  1. Eric Banks

    Merge pull request #558 from broadinstitute/rp_vqsr_nondeterminism_fix

    Fix for non-determinism in the VQSR with very large data sets
    authored
  2. Eric Banks

    Merge pull request #556 from broadinstitute/eb_use_iupac_in_FARM

    Added new functionality to the FastaAlternateReferenceMaker to have it o...
    authored
  3. Eric Banks

    Added new functionality to the FastaAlternateReferenceMaker to have i…

    …t output IUPAC codes for het sites.
    
    Enable it with the new --useIUPAC argument.
    Added both unit and integration tests for the new functionality - and fixed up the
    exising tests once I was in there.
    authored
  4. Ryan Poplin

    Fix for non-determinism in the VQSR with very large data sets

    authored
  5. ldgauthier

    Merge pull request #555 from broadinstitute/eb_add_option_to_CGVCFs_f…

    …or_all_sites_GVCF
    
    Added an option to CombineGVCFs to create basepair resolution gVCFs from...
    authored
  6. Eric Banks

    Merge pull request #557 from broadinstitute/dr_add_warning_for_intel_…

    …pairhmm
    
    Emit a warning whenever the VectorLoglessPairHMM is used
    authored
  7. droazen

    Emit a warning whenever the VectorLoglessPairHMM is used

    authored
  8. Eric Banks

    Added an option to CombineGVCFs to create basepair resolution gVCFs f…

    …rom banded ones.
    
    Use the --convertToBasePairResolution argument to enable this functionality.
    authored

Mar 11, 2014

  1. Ryan Poplin

    Merge pull request #552 from broadinstitute/rp_HaplotypeCaller_1kg_co…

    …nsensus_mode
    
    Added the consensus mode used for the 1000 Genomes Project to the Haplot...
    authored
  2. Ryan Poplin

    Added the consensus mode used for the 1000 Genomes Project to the Hap…

    …lotypeCaller.
    
    -- All the provided alleles are added to the assembly graph as potential haplotypes but they aren't forcibly genotyped like in GGA mode.
    -- Added integration test for this mode
    authored
  3. droazen

    Merge pull request #553 from broadinstitute/dr_rename_pipeline_tests

    Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests
    authored
  4. droazen

    Rename existing PipelineTests to QueueTests to prepare for upcoming p…

    …ush of new pipeline tests
    
    -These tests are really integration tests for Queue rather than generalized
     pipeline tests, so it makes sense to call them QueueTests.
    
    -Rename test classes and maven build targets, and update shell scripts
     to reflect new naming.
    authored

Mar 10, 2014

  1. droazen

    Merge pull request #547 from broadinstitute/intel_pairhmm

    Experimental native PairHMM implementation from Intel. Off by default.
    authored
  2. droazen

    Merge remote-tracking branch 'origin/master' into intel

    authored
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