kiran eb2f0ebd62 If the first base of a read is 'N', and the alignment cigar says every base matches, samtools calls shennanigans. Now I just output an A, but the real way to do this is to modify the cigar string accordingly. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@337 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-08 19:58:18 +00:00
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src/org/broadinstitute/sting	If the first base of a read is 'N', and the alignment cigar says every base matches, samtools calls shennanigans. Now I just output an A, but the real way to do this is to modify the cigar string accordingly.	2009-04-08 19:58:18 +00:00
test/org/broadinstitute/sting	Fixes for shattering, added JUnit test case	2009-04-08 16:37:34 +00:00