depristo 8d13597a27 Temporary command-line support to enable rod walkers, if you know what you are doing this is safe. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2505 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-06 12:15:36 +00:00
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TraversalEngine.java	cleanup of the traversal output code	2009-11-12 06:18:10 +00:00
TraversalStatistics.java	Fixes for including duplicate reads in the locus traversal; now checks that the ref arg is provided when needed	2009-04-17 01:27:36 +00:00
TraverseDuplicates.java	Removed used routines in duputils; duplicatequals to archive; docs for new duplicate traversal code; general code cleanup; bug fixes for combineduplicates; integration tests for combine duplicates walker	2009-12-29 19:46:29 +00:00
TraverseLoci.java	Temporary command-line support to enable rod walkers, if you know what you are doing this is safe.	2010-01-06 12:15:36 +00:00
TraverseLocusWindows.java	some tweaks for the GATK paper genotyper to better work with shared memory parallelization, added documentation changes for Matt's new help system.	2009-12-10 22:33:51 +00:00
TraverseReads.java	Simplify handling of reference sequence for unmapped reads. Improvement made based on a suggestion from Alec.	2009-12-29 21:06:20 +00:00
package-info.java	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00