Joel Thibault 45f64425a3 Update read metrics per shard rather than locus		2012-10-19 15:29:01 -04:00
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alignment	Part II of GSA-462: Consistent RODBinding access across Ref and Read trackers	2012-08-30 10:15:10 -04:00
commandline	Added explicit @ClassType annotations to @Argument for Option[Int] or Option[Double] since scala seems to change the reflected type to Option[Object] on some systems.	2012-10-19 13:20:29 -04:00
gatk	Update read metrics per shard rather than locus	2012-10-19 15:29:01 -04:00
jna	Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc.	2012-01-23 16:17:04 -05:00
queue	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
utils	Actually a better implementation of GATKSAMRecord.getSoftStart(). Last commit was all wrong. Oops.	2012-10-19 12:41:24 -04:00