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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gatk	Added a constructor, took out a copy constructor, and changed some SAMBAM code.	2009-04-08 19:53:20 +00:00
playground	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
utils	Added some stuff for retreiving the base index and probability of a compressed base.	2009-04-08 15:52:58 +00:00
StingException.java	We need a base exception so we can differentiate between exceptions we've generated and those external to our code. All our exceptions should extend this exception. I'll migrate the ones I can find later on.	2009-04-07 00:13:45 +00:00