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
..
old	Restructuring my qscripts	2010-12-11 20:58:45 +00:00
RefineGenotypesAndMerge.q	Commit for Ryan	2010-10-05 19:04:10 +00:00
batchMergePipeline.q	Now that addAll() is in the superclass, no longer need this definition (which, without override, prevents the script from compiling anyway)	2010-12-17 05:36:31 +00:00
expanded_targets.q	Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.	2011-01-07 22:03:36 +00:00
fullCallingPipelineV2.q	java changes:	2010-12-12 05:10:45 +00:00
omni_qc.q	Bug fix to GenotypeConcordance. AC metrics get instantiated based on number of eval samples; if Comp has more samples, we can see AC indeces outside the bounds of the array.	2010-11-03 19:23:03 +00:00
private_mutations.q	PrivatePermutations generalized to compute transition counts and average probabilities (and thus was renamed). Changes in some pipelines to reflect the change. Bugfix in the batch merging pipeline (it would halt because the allele VCF for genotyping batches could become off-spec).	2010-12-22 15:16:15 +00:00