asivache 39e373af6e deleting accidentally committed junk ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4464 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-08 15:13:01 +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
FastqToBam.java	Bug fix from Michael Ross: mark second read in sequence as second of pair.	2009-10-01 14:34:36 +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	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +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