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gatk-3.8/java/src/org/broadinstitute/sting/gatk/datasources/providers
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depristo dfc36c1e95 Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3445 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-05-26 22:12:25 +00:00
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AllLocusView.java Rework the way the MicroScheduler handles locus shards to handle intervals that span shards 2010-03-11 18:40:31 +00:00
CoveredLocusView.java Rework the way the MicroScheduler handles locus shards to handle intervals that span shards 2010-03-11 18:40:31 +00:00
InvalidPositionException.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
LocusReferenceView.java Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK 2010-05-19 23:27:55 +00:00
LocusShardDataProvider.java Rework the way the MicroScheduler handles locus shards to handle intervals that span shards 2010-03-11 18:40:31 +00:00
LocusView.java Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end. 2010-05-26 22:12:25 +00:00
ManagingReferenceOrderedView.java Performance improvements for RODs in conjunction with new sharding system. 2010-03-16 14:54:12 +00:00
RODMetaDataContainer.java The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
ReadBasedReferenceOrderedView.java although holding on to memories can be fun, it's bound to hurt performance. 2010-05-12 19:26:58 +00:00
ReadReferenceView.java Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK 2010-05-19 23:27:55 +00:00
ReadShardDataProvider.java Rework the way the MicroScheduler handles locus shards to handle intervals that span shards 2010-03-11 18:40:31 +00:00
ReadView.java Rework the way the MicroScheduler handles locus shards to handle intervals that span shards 2010-03-11 18:40:31 +00:00
ReferenceOrderedView.java Missing file 2009-09-12 19:17:09 +00:00
ReferenceView.java Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK 2010-05-19 23:27:55 +00:00
RodLocusView.java The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
ShardDataProvider.java Rework the way the MicroScheduler handles locus shards to handle intervals that span shards 2010-03-11 18:40:31 +00:00
View.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
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