chartl 8d0e057d83 I got bored today and decided to write the confusion matrix calculator. At present it is untested. I'm submitting it to subversion to make sure ... I have previous revision to revert back to. This is a calculator that will calculate: P[ True base is X | read base mismatches, secondary base is Y, previous K bases are Z1,Z2,...ZK ] where the number of pervious reference bases to take into account is user-defined. The secondary base is optional as well. --usePreviousBases k tells the walker to use the k previous reference bases in the transition table --useSecondaryBase tells the walker to use the secondary base at a locus in the transition table these can be used together. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1816 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-13 02:55:29 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	I got bored today and decided to write the confusion matrix calculator. At present it is untested. I'm submitting it to subversion to make sure	2009-10-13 02:55:29 +00:00
test/org/broadinstitute/sting	Fix issue Eric was seeing with java.lang.Error in unmap0.	2009-10-09 17:46:56 +00:00