depristo e16bc2cbd9 Contracts for Java now write for GenomeLoc and GenomeLocParser. The semantics of GenomeLoc are now much clearer. It is no longer allowed to create invalid GenomeLocs -- you can only create them with well formed start, end, and contigs, with respect to the mater dictionary. Where one previously created an invalid GenomeLoc, and asked is this valid, you must now provide the raw arguments to helper functions to assess this. Providing bad arguments to GenomeLoc generates UserExceptions now. Added utilty functions contigIsInDictionary and indexIsInDictionary to help with this. ... Refactored several Interval utilties from GenomeLocParser to IntervalUtils, as one might expect they go Removed GenomeLoc.clone() method, as this was not correctly implemented, and actually unnecessary, as GenomeLocs are immutable. Several iterator classes have changed to remove their use of clone() Removed misc. unnecessary imports Disabled, temporarily, the validating pileup integration test, as it uses reads mapped to an different reference sequence for ecoli, and this now does not satisfy the contracts for GenomeLoc git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5827 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-20 15:43:27 +00:00
..
IntervalFileMergingIteratorUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
IntervalIntegrationTest.java	Enable BAM OTF index writing by default.	2011-04-07 23:44:25 +00:00
IntervalUtilsUnitTest.java	Contracts for Java now write for GenomeLoc and GenomeLocParser. The semantics of GenomeLoc are now much clearer. It is no longer allowed to create invalid GenomeLocs -- you can only create them with well formed start, end, and contigs, with respect to the mater dictionary. Where one previously created an invalid GenomeLoc, and asked is this valid, you must now provide the raw arguments to helper functions to assess this. Providing bad arguments to GenomeLoc generates UserExceptions now. Added utilty functions contigIsInDictionary and indexIsInDictionary to help with this.	2011-05-20 15:43:27 +00:00
NwayIntervalMergingIteratorUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00