gatk-3.8

Author	SHA1	Message	Date
kiran	e9be2a9c60	Changed a formatting issue. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1002 348d0f76-0448-11de-a6fe-93d51630548a	2009-06-12 19:40:32 +00:00
kiran	b0cc763eb5	Added some methods to format bases such that read bases on the forward strand are in uppercase, while those on the negative strand are lowercase. This does not affect the default functionality of the standard PileupWalker git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@969 348d0f76-0448-11de-a6fe-93d51630548a	2009-06-10 17:31:00 +00:00
kiran	3adb4239e4	Same as regular Pileup, but also allows you to see flanking region around locus. This will be useful in determining that some SNPs are spurious due to being at the ends of homopolymer regions. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@959 348d0f76-0448-11de-a6fe-93d51630548a	2009-06-10 08:19:31 +00:00