ebanks dd6d61c031 Adding integration test to cover the case of a read that only covers an insertion (i.e. no M in the CIGAR string). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5923 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-02 21:02:47 +00:00
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arguments	A significant refactoring of the ROD system, done largely to simplify the process of	2010-12-31 04:52:22 +00:00
contexts/variantcontext	Contracts for GenomeLocParser and GenomeLoc are now fully implemented.	2011-05-21 02:01:59 +00:00
datasources	Contracts for GenomeLocParser and GenomeLoc are now fully implemented.	2011-05-21 02:01:59 +00:00
executive	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
filters	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
iterators	Some refactoring that Mauricio and I worked through together. Changed filters	2011-05-04 19:29:08 +00:00
refdata	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
report	Added a utility method to retrieve the contig lengths for WG chunking.	2011-04-20 19:22:21 +00:00
traversals	Fix requested by Lee Lichtenstein: first check to see whether it's time for	2011-04-20 03:22:48 +00:00
walkers	Adding integration test to cover the case of a read that only covers an insertion (i.e. no M in the CIGAR string).	2011-06-02 21:02:47 +00:00
GenomeAnalysisEngineUnitTest.java	Contracts for GenomeLocParser and GenomeLoc are now fully implemented.	2011-05-21 02:01:59 +00:00
WalkerManagerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00