depristo 43fdd31e20 Significant performance optimization for reduced reads due to better algorithm for including reads in the variable regions. Fixed a critical bug that actually produced multiple copies of the same read in the variable regions with this optimization as well. Scala exploration script updated as well. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6005 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-16 12:54:59 +00:00
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core	limiting the number of reads in memory for the SamValidateFile.jar	2011-06-10 20:14:30 +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	Significant performance optimization for reduced reads due to better algorithm for including reads in the variable regions. Fixed a critical bug that actually produced multiple copies of the same read in the variable regions with this optimization as well. Scala exploration script updated as well.	2011-06-16 12:54:59 +00:00
playground	Added a samtools merge CLF.	2011-06-03 22:20:38 +00:00