ebanks 8fb37f5f7a For Kiran: warn the user when the actual and vcf ref bases differ so that if an exception is generated later, he knows why. All: should we generate the actual exception here? Is there any reason to allow cases where the vcf record has a different ref base than the actual reference? I'd vote that we die here. Thoughts? ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3680 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-30 13:56:16 +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/org	For Kiran: warn the user when the actual and vcf ref bases differ so that if an exception is generated later, he knows why. All: should we generate the actual exception here? Is there any reason to allow cases where the vcf record has a different ref base than the actual reference? I'd vote that we die here. Thoughts?	2010-06-30 13:56:16 +00:00
test/org/broadinstitute/sting	Added ability to clean using only known indels. Added integration test for it. Fixed vcf->vc conversion for indels which was busted.	2010-06-30 01:20:56 +00:00