aaron 887adcfc7f Some minor fixes to the last check-in ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@387 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-13 18:24:51 +00:00
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dataSources	Some minor fixes to the last check-in	2009-04-13 18:24:51 +00:00
executive	Cleanup, and support either by-interval traversals or full traversals in data source-backed code.	2009-04-10 22:09:01 +00:00
iterators	* refactored GenomeLoc to use contigIndex internally for performance and fixed several calling classes	2009-04-12 02:25:17 +00:00
refdata	a few tweaks to make it more robust: ignore reads with cigars containing anything but I,D,M; don't set up contig ordering manually, rely upon reference sequence and its dictionary; don't die if a record does not have NM tag, but faal back to direct counting instead; now requires reference as a cmdline arg	2009-04-13 04:49:19 +00:00
traversals	TbyLocibyRef previously didn't seem to support traversals with no interval specified. Put in a temporary fix until the threaded approach is in place.	2009-04-10 22:14:06 +00:00
walkers	A class to print out as much context about the given locus site as is possible. Useful for testing traversal engines -- run old and new code across a given region and diff the output to make sure they have the same context.	2009-04-13 15:29:55 +00:00
GenomeAnalysisTK.java	Strictness args are presented as lowercase in the help, but only accepted if uppercase. Changed help to list the valid arguments in uppercase.	2009-04-13 00:50:19 +00:00
LocusContext.java	Added ability to downsample to a particular coverage	2009-04-01 20:27:06 +00:00
WalkerManager.java	Refactor common functionality out of WalkerManager and into JVMUtils and PathUtils. Add support for loading walkers from a jar.	2009-03-30 23:20:55 +00:00