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
..
IntervalFileMergingIterator.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
IntervalMergingRule.java	Refactoring intervals, separating the process of parsing interval lists,	2010-04-13 15:50:38 +00:00
IntervalSetRule.java	providing a way to specify how you'd like -BTI combined with your -L options; set BTIMR to either UNION (default) or INTERSECTION.	2010-08-09 14:00:52 +00:00
IntervalUtils.java	Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.	2011-01-07 22:03:36 +00:00
NwayIntervalMergingIterator.java	N-Way-Out is back. Now uses SAMReadID to identify each read's source bam, so should be reliable. Interface is sort of ugly fo now: to generate output file names, .bam is stripped from input file names, then the value of -nWayOut argument is pasted on (and all the output files are written into the current dir).	2010-11-01 16:06:51 +00:00
OverlappingIntervalIterator.java	bug fix	2010-10-15 16:27:40 +00:00