carneiro 9c1b8ea796 Updated BQSR script to be more general and work with the new PacBio BAM files - for Kristian Cibulskis ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6075 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-23 21:05:28 +00:00
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core	quick memory upgrade to BWA classes.	2011-06-23 20:53:32 +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	Updated BQSR script to be more general and work with the new PacBio BAM files - for Kristian Cibulskis	2011-06-23 21:05:28 +00:00
playground	[Foiled yet again when trying to do this in git] Slight modifications in the argument structure for the IndelRealigner. Instead of boolean flags -knownsOnly and -doNotUseSW, we now have an enum --consensusDeterminationModel which lets you specify knowns only, also use indels in reads, or also use SW. Please note that the default behavior of IR has not changed at all (and won't for a few more days) - that'll be done in GIT (fingers crossed).	2011-06-16 17:35:37 +00:00