hanna 85037ab13f Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of ... Picard patch, including move of some of the Picard private classes we use to Picard public. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3087 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-29 03:21:27 +00:00
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vcf	Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of	2010-03-29 03:21:27 +00:00
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
BamToFastq.java	A standalone companion to BamToFastqWalker: does the same thing but without calling in gatk's heavy artillery (does not "require" a reference either). Extracts seqs and quals and places them into fastq; along the way it also reverse complements reads that align to the negative strand (so that fastq contains reads as they come from the machine).	2009-08-12 20:24:37 +00:00
CGUtilities.java	Simple utilities for dealing with Complete Genomics data	2009-12-02 22:51:41 +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	Very early, half-baked version. All it can do right now is to take two SAM files with end1 and end2 individual single-end alignmnets from a pair-end run and spit out a "paired" BAM file that contains ONLY properly paired ends (both ends align uniquely && both ends align to the same chromosome && the ends align in proper orientation). Insert size is currently not used (and not set in the output). Unpaired/unmapped reads are NOT transferred into the output bam. For the pairs that do get written, the output is (should be) standard-conforming: all flags are properly set and mate pair information is correct.	2009-09-16 18:38:18 +00:00
RemapAlignments.java	Bug fix: single unmapped read now keeps mapping qual 0 after remapping, not 37!	2009-09-09 15:29:34 +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