chartl e5ef8388fc BatchMerge - AlleleVCF --> AllelesVCF, this (combined with Eric's fix) will solve James P.'s forum issue. ... After viewing results on real case/control data from RAW -- it's really working quite well. ReadIndels, however, needs to use a T-test rather than a U-test, especially in deep coverage (at indel sites, the reads with indels will have mostly the same number of CIGAR indel elements -- one -- which doesn't really play nicely with the UTest when sample sets are large). Modified ReadsLargeInsertSize to be a two-way test (e.g. ReadsLarge and ReadsSmall). BaseQualityScore also suffers from the same issue as read indels, so switching over to a T-test in that case as well. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5653 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-15 22:03:16 +00:00
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core	bug fix in MDCP	2011-04-11 18:27:47 +00:00
examples	When /etc/mailname is unreadable fall back to the hostname.	2011-04-11 20:22:44 +00:00
lib	Thanks to mark: VCFInfoToTable removed in favor of a more flexible walker. Slight change to the argument structure of the walker to make it play more nicely with Queue: the field list parsing is pushed into the command line system (e.g. the variable is exposed as a List<String> and not a String, so Queue doesn't have to join a list into a string only to have it broken out again. This also allows the user to specify -F field1 -F field2 -F field3 if he/she so desires.	2010-12-15 03:33:36 +00:00
oneoffs	Old changes to the exome VQSR search.	2011-04-12 23:00:50 +00:00
playground	BatchMerge - AlleleVCF --> AllelesVCF, this (combined with Eric's fix) will solve James P.'s forum issue.	2011-04-15 22:03:16 +00:00