kiran 25474ebe7e Computes the read error rate for a bam file. Ignores reads with indels, treats low-quality and high-quality reference bases the same. Does not count ambiguous reference bases as mismatches. Optionally allows for best two bases in read to be used. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@330 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-08 15:56:10 +00:00
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src/org/broadinstitute/sting	Computes the read error rate for a bam file. Ignores reads with indels, treats low-quality and high-quality reference bases the same. Does not count ambiguous reference bases as mismatches. Optionally allows for best two bases in read to be used.	2009-04-08 15:56:10 +00:00
test/org/broadinstitute/sting/utils/cmdLine	Fix argument parser test case.	2009-03-27 16:05:18 +00:00