hanna 76efa757f0 Switched over to reviewed version of Picard patch. In process, did some optimization to the IntervalSharder ... which improved startup time 5-10x when dynamically merging many BAMs. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3331 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-08 14:12:22 +00:00
..
BAMFormatAwareShard.java	Revisions to take into account finalization of Picard patch: naming changes, better definition	2010-03-30 19:28:14 +00:00
BlockDelimitedReadShard.java	Revisions to take into account finalization of Picard patch: naming changes, better definition	2010-03-30 19:28:14 +00:00
BlockDelimitedReadShardStrategy.java	Revisions to take into account finalization of Picard patch: naming changes, better definition	2010-03-30 19:28:14 +00:00
IndexDelimitedLocusShard.java	Revisions to take into account finalization of Picard patch: naming changes, better definition	2010-03-30 19:28:14 +00:00
IndexDelimitedLocusShardStrategy.java	Revisions to take into account finalization of Picard patch: naming changes, better definition	2010-03-30 19:28:14 +00:00
IntervalShard.java	Basic support for very simple index-driven locus traversals. Interface has been changed to	2010-01-29 03:14:26 +00:00
IntervalShardStrategy.java	removed the dependence on removeRegion() in GenomeLocSortedSet	2010-03-12 22:35:49 +00:00
IntervalSharder.java	Switched over to reviewed version of Picard patch. In process, did some optimization to the IntervalSharder	2010-05-08 14:12:22 +00:00
LinearLocusShardStrategy.java	Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.	2009-06-11 18:13:22 +00:00
LocusShard.java	Got back most of the performance lost when I fixed the dropped reads problem.	2010-02-12 19:59:56 +00:00
LocusShardStrategy.java	removed the dependence on removeRegion() in GenomeLocSortedSet	2010-03-12 22:35:49 +00:00
MonolithicShard.java	Basic support for very simple index-driven locus traversals. Interface has been changed to	2010-01-29 03:14:26 +00:00
MonolithicShardStrategy.java	Temporary hack for Tim Fennell: introduce a sharding strategy that stuffs all data into a single	2009-12-16 21:55:42 +00:00
ReadDelimitedReadShard.java	First successful test of new sharding system prototype. Can traverse over reads from a single	2010-01-15 03:35:55 +00:00
ReadDelimitedReadShardStrategy.java	Oops! Introduced a performance bug in read interval sharding, when the new sharding system is available. Track more state to avoid this problem in the future.	2010-03-11 23:19:42 +00:00
ReadOverlapFilter.java	Support for read interval sharding with proper filtering.	2010-02-27 20:26:34 +00:00
ReadShard.java	Basic support for very simple index-driven locus traversals. Interface has been changed to	2010-01-29 03:14:26 +00:00
ReadShardStrategy.java	First successful test of new sharding system prototype. Can traverse over reads from a single	2010-01-15 03:35:55 +00:00
Shard.java	Basic support for very simple index-driven locus traversals. Interface has been changed to	2010-01-29 03:14:26 +00:00
ShardStrategy.java	First successful test of new sharding system prototype. Can traverse over reads from a single	2010-01-15 03:35:55 +00:00
ShardStrategyFactory.java	A few stopgap fixes to get the GATK to the point where the old sharding	2010-03-07 21:01:25 +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