hanna 46c14ec63f New, much less memory intensive implementation of BAM file sharding. Streams indices together with the expectation ... that bins will be present in the bin sparse array, which avoids the problem of having to hold the sparse bin array stored in every BAM file index in memory at the same time. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3075 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-25 17:41:22 +00:00
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providers	Fixing the bug introduced with the earlier commit. When trimming locus to the current bases, we need to take into account expanded boundaries (for windowed reference traversals)	2010-03-22 19:20:34 +00:00
shards	New, much less memory intensive implementation of BAM file sharding. Streams indices together with the expectation	2010-03-25 17:41:22 +00:00
simpleDataSources	Phase 2 of Picard patch refactoring: kill off SAMFileReader2/BAMFileReader2, merging the changes back into the base classes.	2010-03-23 16:48:11 +00:00
BAMFileStat.java	Changing preloaded index to only "preload" reference sequences on demand.	2010-03-23 22:02:28 +00:00
DataSourceGenerationException.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