chartl dfa3c3b875 Added: ... SequenomToVCF - Takes a sequenom ped file and converts it to a VCF file with the proper metrics for QC. It's currently a rough draft, but is working as expected on a test ped file, which is included as an integration test. Modified: VCFGenotypeCall -- added a cloneCall() method that returns a clone of the call Hapmap2VCF -- removed a VCFGenotypeCall object that gets instantiated and modified but never used (caused me all kinds of confusion when I was basing SequenomToVCF off of it) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2554 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-11 17:17:21 +00:00
..
alignment	Support for ad-hoc reference sequences. Also reenabled BWA/Java integration test, which was commented out	2010-01-02 20:19:14 +00:00
gatk	Fixing another bug in solid recal regarding negative strand reads. The isInconsistentColorSpace method incorrectly used the inconsistent tag added by parseColorSpace, the inconsistent tag is in the direction of the read like the color space tag, and not in the direction of the reference like everything else. This affects the recalibrated quality scores but the improvment in SNP calling performance is minor when using the default UG settings (min base quality 10).	2010-01-11 14:28:52 +00:00
playground/gatk/walkers	Added:	2010-01-11 17:17:21 +00:00
utils	Minor interface change for VCFGenotypeRecord.	2010-01-07 16:48:09 +00:00
BaseTest.java	moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.	2009-12-29 07:40:48 +00:00
TrivialInstrumenter.java	fixed a bunch of comments and license headers.	2009-06-10 14:10:46 +00:00
WalkerTest.java	Added the capability to allow expressions in an integration test command (i.e. -filter 'foo') by escaping them in the command.	2009-11-24 02:34:48 +00:00