Eric Banks 99d27ddcc4 Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now.		2012-04-02 14:27:36 -04:00
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providers	Documentation request by Eric. At each stage of the GATK where filtering occurs, added documentation suggesting the goal of the filtering along with examples of suggested inputs and outputs.	2012-02-09 11:24:52 -05:00
reads	Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now.	2012-04-02 14:27:36 -04:00
reference	'Fixing' the changes in ReferenceDataSource so that a shard properly contains a list of GenomeLocs instead of a single merged one. However, that uncovered a probable bug in the engine, so instead of letting this code fester unfixed in the build (affecting everyone in the group) I've decided to revert the previous (slow, but working) version and fix the engine in my own branch.	2011-12-23 15:39:12 -05:00
rmd	Found the bug in the engine: RodLocusView was using the wrong seek method so that it would only move to the first locus of a shard (and with multi-locus shards, this meant that we never processed RODs from the other positions). In fact, because the seek(Shard) method is extremely misleading and now no longer used, I think it's safer to delete it and make everyone use the much more transparent seek(GenomeLoc). Note that I have not re-enabled my improvements to the intervals accumulation of ReferenceDataSource because that inefficiency is still present downstream in RodLocusView; need to discuss those changes with Matt.	2011-12-26 14:45:19 -05:00
package-info.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00