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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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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
..
datasources SAMReaderID: fix bug with hash code and equals() method 2013-07-15 13:57:00 -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 Detect stuck lock-acquisition calls, and disable file locking for tests 2013-04-24 22:49:02 -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 Exclude reduced reads from elimination during downsampling 2013-06-11 16:16:26 -04:00
walkers SAMDataSource: always consolidate cigar strings into canonical form 2013-06-19 13:29:01 -04:00
CommandLineGATKUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
EngineFeaturesIntegrationTest.java Better GATK version and command line output 2013-06-20 11:19:13 -04:00
GenomeAnalysisEngineUnitTest.java SAMReaderID: fix bug with hash code and equals() method 2013-07-15 13:57:00 -04:00
MaxRuntimeIntegrationTest.java Subshard timeouts in the GATK 2013-05-15 07:00:39 -04:00
ReadMetricsUnitTest.java Implement ActiveRegionTraversal RefMetaDataTracker for map call; HaplotypeCaller now annotates ID from dbSNP 2013-06-10 16:20:31 -04:00
WalkerManagerUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00