aaron 2e4949c4d6 Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1751 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-30 20:37:59 +00:00
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AllLocusViewTest.java	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
CoveredLocusViewTest.java	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
LocusReferenceViewTest.java	Windowed access to the reference.	2009-08-05 16:29:15 +00:00
LocusViewTemplate.java	Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.	2009-09-30 20:37:59 +00:00
ReadReferenceViewTest.java	When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions.	2009-06-29 20:51:55 +00:00
ReferenceOrderedViewTest.java	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +00:00
ReferenceViewTemplate.java	Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.	2009-06-22 14:39:41 +00:00
ShardDataProviderTest.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