chartl be31d7f4cc Added - a walker that outputs relevant information about false negatives given a bunch of hapmap individuals and corresponding integration tests for it. ... This will output for hapmap variant sites: chromosome position ref allele variant allele number of variant alleles of the individuals depth of coverage power to detect singletons at lod 3 number of variant bases seen whether or not variant was called git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2068 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-18 15:47:52 +00:00
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alignment	Finally reinstate the iterator-style interface. Get rid of some scaffolding code.	2009-11-16 02:34:19 +00:00
gatk	Rollback of the previous "fix" and implementation of the real fix.	2009-11-18 06:09:24 +00:00
playground	Added - a walker that outputs relevant information about false negatives given a bunch of hapmap individuals and corresponding integration tests for it.	2009-11-18 15:47:52 +00:00
secondarybase	Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.	2009-09-30 20:37:59 +00:00
utils	Ignoring deletions in the primary pileup by default was causing the primary pileup to become shorter than the secondary pileup when building up the secondary base pileup string. This fix makes sure to include the primary Ds within the pileup so that not only are the pileups guaranteed to be the same size, the same offsets will truly correspond with the same read.	2009-11-17 17:20:13 +00:00