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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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Michael McCowan c3a933ce84 Adaptations to accomodate Tribble API changes, comprising mostly of the following. 
* Refactoring implementations of readHeader(LineReader) -> readActualHeader(LineIterator), including nullary implementations where applicable.
* Galvanizing fo generic types.
* Test fixups, mostly to pass around LineIterators instead of LineReaders.
* New rev of tribble, which incorporates a fix that addresses a problem with TribbleIndexedFeatureReader reading a header twice in some instances.
* New rev of sam, to make AbstractIterator visible (was moved from picard -> sam in Tribble API refactor).
 		2013-08-19 15:52:47 -04:00
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datasources GATK engine: add ability to do on-the-fly BAM file sample renaming at runtime 2013-07-18 15:48:42 -04:00
downsampling Exclude reduced reads from elimination during downsampling 2013-06-11 16:16:26 -04:00
executive Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters This commit addresses JIRA issue GSA-948: Prevent users from doing the wrong thing with RNA-Seq data and the GATK. 2013-06-10 10:44:42 -04:00
iterators SAMDataSource: always consolidate cigar strings into canonical form 2013-06-19 13:29:01 -04:00
refdata Adaptations to accomodate Tribble API changes, comprising mostly of the following. 2013-08-19 15:52:47 -04:00
report Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
samples Trivial update to ceutrio.ped file to make it really the CEU trio sample names 2013-05-14 17:08:13 -04:00
traversals GATK engine: add ability to do on-the-fly BAM file sample renaming at runtime 2013-07-18 15:48:42 -04:00
walkers moved SnpEffUtilUnitTest to public tree 2013-07-30 17:51:40 -04:00
CommandLineGATKUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
EngineFeaturesIntegrationTest.java Adaptations to accomodate Tribble API changes, comprising mostly of the following. 2013-08-19 15:52:47 -04:00
GenomeAnalysisEngineUnitTest.java GATK engine: add ability to do on-the-fly BAM file sample renaming at runtime 2013-07-18 15:48:42 -04:00
MaxRuntimeIntegrationTest.java Subshard timeouts in the GATK 2013-05-15 07:00:39 -04:00
ReadMetricsUnitTest.java GATK engine: add ability to do on-the-fly BAM file sample renaming at runtime 2013-07-18 15:48:42 -04:00
WalkerManagerUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00