hanna 8e36a07bea Convert GenomeLocParser into an instance variable. This change is required ... for anything that needs to be simultaneously aware of multiple references, eg Queue's interval sharding code, liftover support, distributed GATK etc. GenomeLocParser instances must now be used to create/parse GenomeLocs. GenomeLocParser instances are available in walkers by calling either -getToolkit().getGenomeLocParser() or -refContext.getGenomeLocParser() This is an intermediate change; GenomeLocParser will eventually be merged with the reference, but we're not clear exactly how to do that yet. This will become clearer when contig aliasing is implemented. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4642 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-10 17:59:50 +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	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +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