kiran 6db9a00a0b SAMFileWriter doesn't appear to flush the buffer when its destructor is called. You have to call the close() method. Also, choose a random base for Ns in the forward and reverse strands so that samtools doesn't pitch a fit. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@338 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-08 21:48:24 +00:00
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src/org/broadinstitute/sting	SAMFileWriter doesn't appear to flush the buffer when its destructor is called. You have to call the close() method. Also, choose a random base for Ns in the forward and reverse strands so that samtools doesn't pitch a fit.	2009-04-08 21:48:24 +00:00
test/org/broadinstitute/sting	Fixes for shattering, added JUnit test case	2009-04-08 16:37:34 +00:00