kshakir b34e2f733f Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list. ... Updated the Queue scatter/gather for read walkers to include -L unmapped on the last scatter job when intervals aren't specified, and to map it correctly when it is explicitly set. Simplified the build.xml/ivy.xml to fix a bug reported with "ant clean dist test" where the scalac target wasn't found. Now building all scala code at the same time, just like all java code is compiled at the same time. Sped up the build for everyone by uncommenting a small bit of classes so that javac/scalac will not constantly launch trying to build .class files that will never compile. Moved some source files to their expected location so that the .java/.scala -> .class is a one-to-one match, again keeping the compilers from wasting cycles. Used <uptodate> and <touch> to skip extracting the help text and generating the GATK Queue extensions when the source files haven't been modified. Fixed a couple errors when the <javadoc> task is run. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4963 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-07 22:03:36 +00:00
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carneiro	Implemented a new argument (-DQS --defaultQualityScore) that allows GATK to deal with BAM files missing quality scores. If a value is specified, all reads are filled with the default quality score. Appropriate exception is thrown if -DQS is not provided and BAM file doesn't have quality scores for every base.	2011-01-05 22:25:08 +00:00
chartl	Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.	2011-01-07 22:03:36 +00:00
depristo	phasing per sample. tmp checkin	2010-12-22 20:14:06 +00:00
examples	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.	2010-10-21 06:37:28 +00:00
hanna	Trying out Queue for the first time.	2010-11-18 18:29:12 +00:00
kshakir	Checking in scripts used for testing the linear index MAX_FEATURES_PER_BIN.	2010-12-20 21:25:36 +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
rpoplin	In the Methods development pipeline the call confidence threshold must be lowered from the default value for lowpass calling. What a bone-headed mistake!	2011-01-05 20:30:55 +00:00
fullCallingPipeline.q	Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.	2011-01-07 22:03:36 +00:00
recalibrate.scala	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.	2010-10-21 06:37:28 +00:00