David Roazen c15751e41e SAMReaderID: fix bug with hash code and equals() method ... -Two SAMReaderIDs that pointed at the same underlying bam file through a relative vs. an absolute path were not being treated as equal, and had different hash codes. This was causing problems in the engine, since SAMReaderIDs are often used as the keys of HashMaps. -Fix: explicitly use the absolute path to the encapsulated bam file in hashCode() and equals() -Added tests to ensure this doesn't break again		2013-07-15 13:57:00 -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	SAMReaderID: fix bug with hash code and equals() method	2013-07-15 13:57:00 -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	A whole slew of improvements to the Haplotype Caller and related code.	2013-07-12 10:09:10 -04:00
BaseTest.java	Working version of HaplotypeCaller ReferenceConfidenceModel that accounts for indels as well as SNP confidences	2013-07-02 15:46:38 -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