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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commandline	Fixed the logic of the @Output annotation and its interaction with 'required'.	2013-03-14 11:58:51 -04:00
gatk	Adaptations to accomodate Tribble API changes, comprising mostly of the following.	2013-08-19 15:52:47 -04:00
jna	Fix pipeline tests that were not respecting the pipeline test dry run setting	2013-06-28 15:27:17 -04:00
utils	Adaptations to accomodate Tribble API changes, comprising mostly of the following.	2013-08-19 15:52:47 -04:00
BaseTest.java	Adaptations to accomodate Tribble API changes, comprising mostly of the following.	2013-08-19 15:52:47 -04:00
ExampleToCopyUnitTest.java	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00
MD5DB.java	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
MD5Mismatch.java	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
StingTextReporter.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -05:00
WalkerTest.java	Reduce number of leftover temp files in GATK runs	2013-06-14 15:56:03 -04:00