asivache 2fb45dbd73 Make window size a command line argument ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1967 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-03 16:13:35 +00:00
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CleanedReadInjector.java	Hash by chromosome for now to reduce memory. This is a temporary solution until we decide how to reture the Injector for good.	2009-10-07 20:06:25 +00:00
IndelGenotyperV2Walker.java	Make window size a command line argument	2009-11-03 16:13:35 +00:00
IndelGenotyperWalker.java	All walkers now use read.getReadGroup()	2009-10-14 19:27:40 +00:00
IndelIntervalWalker.java	oops - we don't need reference bases, but we still need reference	2009-09-18 16:24:45 +00:00
IntervalCleanerWalker.java	Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.	2009-09-30 20:37:59 +00:00
IntervalMergerWalker.java	After thinking about this a bit more, it makes sense to pull this functionality out of my walker and into the GenomeLocParser where everyone else can benefit from it...	2009-09-22 01:32:35 +00:00
MismatchIntervalWalker.java	Bug fix: when jumping onto next contig (chromosome), the walker was erasing last mismatch interval from the previous chr it was still holding without printing it; now it gets printed.	2009-09-25 22:24:34 +00:00
SNPClusterWalker.java	Removing the AllelicVariant interface, which is replaced by the Variation interface.	2009-10-06 17:44:24 +00:00