aaron 03f8177a53 When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1121 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-29 20:51:55 +00:00
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gatk	When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions.	2009-06-29 20:51:55 +00:00
playground/gatk/walkers/indels	First pass at passing lists of files / lists of interval arguments work. Note that the interval	2009-06-25 20:44:23 +00:00
utils	Some files to support generic genotype outputing	2009-06-26 15:43:41 +00:00
BaseTest.java	Added some code to change the instrumentation for tests.	2009-05-20 05:15:27 +00:00
TrivialInstrumenter.java	fixed a bunch of comments and license headers.	2009-06-10 14:10:46 +00:00