ebanks 4fe0fcd707 Updates to handle CG data, headers, etc. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5215 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-08 03:16:05 +00:00
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BCMMarkDupes.java	Matthew Bainbridge's duplicate removal utility for 454 data. This code should eventually be moved into a read walker. For now, it's being introduced into the repository as-is (well, with one minor change to make the handling of command-line arguments a little more straightforward).	2009-10-08 18:32:37 +00:00
FilterReads.java	A very simple standalone filter for fooling around with the data: can extract only mapped or only unmapped reads, only reads with mapping quals > X, reads with average base qual > Y, reads with min base qual > Z, reads with edit distance from the ref > MIN and/or < MAX	2009-08-12 20:28:51 +00:00
PairMaker.java	deleting accidentally committed junk	2010-10-08 15:13:01 +00:00
RemapAlignments.java	If among all the multiple alignments for the given read we have 'unmapped' ones (can happen with bwa 0.5.7 and maybe later versions), then discard the latters and keep only the mapped ones. Keep 'unmapped' only if its the only alignment available.	2011-01-26 20:07:08 +00:00
SortROD.java	Updates to handle CG data, headers, etc.	2011-02-08 03:16:05 +00:00
SplitReads.java	be nice, don't forget to close the reader when done	2009-08-12 20:19:56 +00:00
VcfToGeliText.java	Naive tool to convert from vcf to geli text	2009-09-13 17:25:02 +00:00