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annotator
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Removing the Genomic Annotator and its supporting classes
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2011-07-25 15:10:25 -04:00 |
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beagle
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This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation.
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2011-07-12 14:11:53 -04:00 |
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coverage
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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diffengine
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Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable"
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2011-07-19 18:38:53 -04:00 |
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fasta
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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filters
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This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation.
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2011-07-12 14:11:53 -04:00 |
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genotyper
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The Unified Genotyper now does NOT emit SLOD/SB by default; to compute SB use --computeSLOD
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2011-08-02 10:14:21 -04:00 |
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indels
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Adding back temporarily removed integration test now that the file permissions have been fixed.
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2011-08-02 12:39:11 -04:00 |
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phasing
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Updated MD5 for PhaseByTransmissionIntegrationTest
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2011-07-26 17:52:25 -04:00 |
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qc
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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recalibration
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Adding MappingQualityUnavailableReadFilter to the SNP and indel CountCovariates
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2011-07-12 15:39:07 -04:00 |
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validation
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When using the BWA bindings, you have to explicitly call close() to get the
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2011-07-21 12:13:29 -04:00 |
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varianteval
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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variantrecalibration
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Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.
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2011-07-18 10:46:01 -04:00 |
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variantutils
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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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BAQIntegrationTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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ClipReadsWalkersIntegrationTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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PileupWalkerIntegrationTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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PrintReadsIntegrationTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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PrintReadsWalkerUnitTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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