depristo 9a1d0d7076 Simple bug fix to allow multiple records at same site when genotyping given alleles. Takes only the first record (respecting filters, SNP type, etc), and issues a warning if there is more than one valid record at a site ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5789 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-11 14:17:14 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Simple bug fix to allow multiple records at same site when genotyping given alleles. Takes only the first record (respecting filters, SNP type, etc), and issues a warning if there is more than one valid record at a site	2011-05-11 14:17:14 +00:00
test	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