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gatk-3.8/java/test/org/broadinstitute/sting/gatk/datasources/providers
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hanna 21d1eba502 Cleaned division of responsibilities between arguments to map function. Reference has been changed 
from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-08-04 21:01:37 +00:00
..
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 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. Now with a test case! 2009-07-02 14:15:50 +00:00
LocusViewTemplate.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +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 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
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