chartl 863d3023d5 IndelCounterWalker -- a new little walker that counts indels over a region (want to see what kind of havoc BWA may be resulting in). Don't know when BasicPileup.indelPileup() was written, but kudos to whoever wrote it. ... BTTJ - remove 'N's from previous base analysis -- even if both read and ref are 'N' (which does happen, occasionally) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1925 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-28 19:50:50 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	IndelCounterWalker -- a new little walker that counts indels over a region (want to see what kind of havoc BWA may be resulting in). Don't know when BasicPileup.indelPileup() was written, but kudos to whoever wrote it.	2009-10-28 19:50:50 +00:00
test/org/broadinstitute/sting	a fix for traverse dupplicates bug: GSA-202. Also removed some debugging output from FastaAltRef walker	2009-10-26 20:18:55 +00:00