hanna ee9077fc69 LocusIterator iterated through LocusContexts, which was fine until now when we need something ... that iterates through loci (GenomeLocs). Rename LocusIterator to LocusContextIterator. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@662 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-12 13:54:57 +00:00
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providers	LocusIterator iterated through LocusContexts, which was fine until now when we need something	2009-05-12 13:54:57 +00:00
shards	Changes to the interface to the simple data source rippled out to a bunch of files.	2009-04-30 20:35:56 +00:00
simpleDataSources	a fix for a situation where a chromosome on the reference file contains no reads, and doesn't align to the bam file. This came up using reference 18, which has chomosomes like chr1_random that aren't in all BAM files.	2009-05-11 01:39:25 +00:00
DataSourceGenerationException.java	Exception cleanup. All our non-runtime exceptions should extend from StingException, StingException needs to be lower in the tree to build.	2009-04-16 22:17:25 +00:00
ReadDataSource.java	Moved fasta support files into their own package.	2009-04-14 18:13:23 +00:00