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
..
alignment	Quick fix for Danny Lieber: flesh out the additional functionality required	2011-01-31 05:28:37 +00:00
commandline	Fixed long-standing bug reported by Mauricio where @Arguments assigned to	2011-01-12 22:18:24 +00:00
datasources/pipeline	Removed deprecated getDbsnpFile.	2011-02-08 21:12:15 +00:00
gatk	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
jna	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
oneoffprojects/walkers	PLEASE READ ME! In order to prepare for the upcoming changes to VCF4, we felt it was best to split up the vcf3 and vcf4 codecs (vcf4 is not backwards compatible to vcf3 and certain changes are too complex to handle in both codecs). Using the 'VCF' rod type in the GATK will now throw a UserException for vcf3.2 or vcf3.3 files telling you to use the 'VCF3' type instead (and vice versa). Integration/unit tests have been updated. For programmers: note that there is currently a lot of code duplication in the two codecs (although I pulled out the easy stuff to a VCFCodecUtils class); however WE ARE FREEZING THE VCF3 CODEC AND WILL NO LONGER MAKE CHANGES TO IT. All updates/improvements will be targetted to the vcf4 codec only as vcf3 is there only to be able to read legacy files. People should really be using vcf4 files only.	2011-05-11 12:07:44 +00:00
playground/gatk/walkers	PLEASE READ ME! In order to prepare for the upcoming changes to VCF4, we felt it was best to split up the vcf3 and vcf4 codecs (vcf4 is not backwards compatible to vcf3 and certain changes are too complex to handle in both codecs). Using the 'VCF' rod type in the GATK will now throw a UserException for vcf3.2 or vcf3.3 files telling you to use the 'VCF3' type instead (and vice versa). Integration/unit tests have been updated. For programmers: note that there is currently a lot of code duplication in the two codecs (although I pulled out the easy stuff to a VCFCodecUtils class); however WE ARE FREEZING THE VCF3 CODEC AND WILL NO LONGER MAKE CHANGES TO IT. All updates/improvements will be targetted to the vcf4 codec only as vcf3 is there only to be able to read legacy files. People should really be using vcf4 files only.	2011-05-11 12:07:44 +00:00
utils	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
BaseTest.java	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
StingTextReporter.java	Cleanup testng listener configuration.	2010-11-15 23:43:14 +00:00
WalkerTest.java	Added a utility method to retrieve the contig lengths for WG chunking.	2011-04-20 19:22:21 +00:00