Eric Banks
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27f0748b33
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Renaming the HapMap codec and feature to RawHapMap so that we don't get esoteric errors when trying to bind a rod with the name 'hapmap' (since it was also a feature).
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2011-08-12 11:11:56 -04:00 |
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Eric Banks
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b20c4d5286
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Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.
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2011-08-09 12:04:55 -04:00 |
David Roazen
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b180a1311a
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Merge branch 'snpEff'
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2011-08-08 22:12:14 -04:00 |
Mark DePristo
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80924d24de
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Single positional arguments are now treated as names unless they actually match a tribble feature
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2011-08-08 19:26:27 -04:00 |
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David Roazen
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5e288136e0
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Added unit tests for the SnpEff codec, and made minor adjustments to the codec itself.
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2011-08-08 16:51:43 -04:00 |
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Mark DePristo
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f0d798d47c
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Bug fix: call RodBinding.resetNameCounter() in new ParsingEngine() so that we don't magically misnumber arguments in the integration tests where the GATK is only instantiated once.
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2011-08-04 12:06:10 -04:00 |
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Mark DePristo
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79e4a8f6d3
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Merge
Conflicts:
private/java/src/org/broadinstitute/sting/gatk/walkers/qc/TestVariantContextWalker.java
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
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2011-08-03 15:09:47 -04:00 |
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Mark DePristo
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b25140db83
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Contracts and documentation for some of RefMetaDataTracker
Continuing to fix integration tests that don't pass / run
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2011-08-03 13:34:20 -04:00 |
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Eric Banks
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7c89fe01b3
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Instead of having the padded reference base be some hackish attribute it is now an actual variable in the Variant Context class. More importantly, we now always require that it be present when padding is necessary - and validate as such upon construction of the VC. This cleans up the interface significantly because we no longer require that a reference base be passed in when writing a VC/VCF record.
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2011-08-03 11:00:36 -04:00 |
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Mark DePristo
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83891271b5
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--variants throughout integrationtests
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2011-08-02 20:28:47 -04:00 |
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Mark DePristo
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eacf205f40
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Tests needed to be updated to reflect the code reorg of tribble.
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2011-07-16 09:22:34 -04:00 |
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Eric Banks
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6a431da554
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Don't output source and ref header lines anymore. Short-term motivation for this is that I'd like this tool when run on a VCF to emit the exact same VCF. Long-term motivation is that these tags should be output by the VCF writer itself for all tools.
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2011-07-13 14:40:01 -04:00 |
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David Roazen
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f18fffd625
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Fixing broken paths to the testdata directory throughout the codebase.
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2011-06-29 17:36:47 -04:00 |
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David Roazen
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3c9497788e
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Reorganized the codebase beneath top-level public and private directories,
removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
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2011-06-28 06:55:19 -04:00 |