asivache 4e62de4213 Added method getOriginalReadGroupId(): takes merged (in case of collision) read group id as reported by a read coming from the merged stream and returns this read's read group id as it was listed in the original input bam file. ... IndelRealigner now uses this functionality to correctly un-mangle read group id's in --nWayOut mode (i.e. when we need to write reads into separate output bams with headers matching the original inputs). Some hidden changes to IndelRealigner: purely testing and development, transparent to the users (hidden option added) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4775 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-02 21:41:52 +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	Added method getOriginalReadGroupId(): takes merged (in case of collision) read group id as reported by a read coming from the merged stream and returns this read's read group id as it was listed in the original input bam file.	2010-12-02 21:41:52 +00:00
test	Bug fix in CountCovariates, skip over indel records as well as SNPs in the dbsnp file. CountCovariates is now called CountCovariatesWalker. I've always hated that the name was swapped.	2010-12-02 18:43:24 +00:00