Mauricio Carneiro c210b7cde4 Merge GATK repo into CMI-GATK ... Bringing in the following relevant changes: * Fixes the indel realigner N-Way out null pointer exception DEV-10 * Optimizations to ReduceReads that bring the run time to 1/3rd. Conflicts: protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java DEV-10 #resolve #time 2m		2012-10-23 10:59:11 -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	Merge GATK repo into CMI-GATK	2012-10-23 10:59:11 -04:00
jna	…
queue	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
utils	Better error message when generic types are erased from scala collections.	2012-10-22 16:27:31 -04:00