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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providers	Implement ActiveRegionTraversal RefMetaDataTracker for map call; HaplotypeCaller now annotates ID from dbSNP	2013-06-10 16:20:31 -04:00
reads	SAMReaderID: fix bug with hash code and equals() method	2013-07-15 13:57:00 -04:00
reference	Remove auto-creation of fai/dict files for fasta references	2013-04-02 18:34:08 -04:00
rmd	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00