kshakir 2ef66af903 Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high. ... Moved the BamListWriter from FCP to ListWriterFunction in the Queue core. Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s. Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-28 23:33:58 +00:00
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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	Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high.	2011-01-28 23:33:58 +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