Mauricio Carneiro 75783af6fc int <-> BitSet conversion utils for MathUtils ... * added unit tests.		2012-02-21 14:10:36 -05:00
..
alignment	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
analyzecovariates	Active Region Traversal should use GATKSAMRecords everywhere instead of SAMRecords. misc cleanup.	2012-02-03 17:13:52 -05:00
commandline	Merged bug fix from Stable into Unstable	2012-01-23 12:08:39 -05:00
gatk	Redid fix for corner case when forming consensus with reads that start/end with insertions and that don't agree with each other in inserted bases: since I can't iterate over the elements of a HashMap because keys might change during iteration, and since I can't use ConcurrentHashMaps, the code now copies structure of (bases, number of times seen) into ArrayList, which can be addressed by element index in order to iterate on it.	2012-02-20 09:12:51 -05:00
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	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
utils	int <-> BitSet conversion utils for MathUtils	2012-02-21 14:10:36 -05:00