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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clf/vcf	One more little bfix -- the issue was not the grep command, but instead the NFS in the awk; i changed it to ++count in the last commit which was really responsible for the fix. Then this ultra-escaping semi-broke teh grep again.	2010-12-13 20:36:14 +00:00
ipf	Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.	2011-01-07 22:03:36 +00:00