kshakir 8619f49d20 Added a utility method to retrieve the contig lengths for WG chunking. ... Added a rudimentary GATKReportParser for parsing VE3 results. Re-enabled the FCPTest using VE3, the GATKRP, and the PicardAggregationUtils. The tag type for .rod files is DBSNP, not ROD. More explicit return types on implicit methods. Added null checks for implicit string to/from file conversions. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5668 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-20 19:22:21 +00:00
..
IntervalFileMergingIterator.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
IntervalMergingRule.java	Refactoring intervals, separating the process of parsing interval lists,	2010-04-13 15:50:38 +00:00
IntervalSetRule.java	providing a way to specify how you'd like -BTI combined with your -L options; set BTIMR to either UNION (default) or INTERSECTION.	2010-08-09 14:00:52 +00:00
IntervalUtils.java	Added a utility method to retrieve the contig lengths for WG chunking.	2011-04-20 19:22:21 +00:00
NwayIntervalMergingIterator.java	N-Way-Out is back. Now uses SAMReadID to identify each read's source bam, so should be reliable. Interface is sort of ugly fo now: to generate output file names, .bam is stripped from input file names, then the value of -nWayOut argument is pasted on (and all the output files are written into the current dir).	2010-11-01 16:06:51 +00:00
OverlappingIntervalIterator.java	bug fix	2010-10-15 16:27:40 +00:00