chartl 2bc5971ca1 Added - a tool to fix reference bases of a VCF. The OMNI had a couple of sites with incorrect reference bases (look to be legacy from other chips), and a few more that had ref and alt flipped. GAP should probably take care of it, but since I need results by monday, I'm doing it. ... Modified - SelectVariants: Hook up to VariantContextUtils to recalculate AC/AF/AN, which uses the accessor in VariantContext to do this. Somehow sites that were selected down to hom-ref genotypes only wound up getting positive AC. **IMPORTANT** I kind of need input here. The header of a file used for an integration test specifies AC as being an integer. Recalculating it casts it into an integer list (which it should be, as it allows for alternate alleles). However this appears to clash with what the jexl expression is looking for? For now, the integration test itself needed to be changed -- it's unclear what to do when the header specifies AC of being one class, but recalculating it casts to another class, and I'm not sure what to do. I'm committing my omni_qc pipeline because I'm almost certain 2 months down the road I'm going to wonder what the heck I did to generate my results. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4511 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-17 03:18:01 +00:00
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alignment	all fixed..thanks Matt!	2010-09-10 06:18:59 +00:00
commandline	Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.	2010-09-12 15:07:38 +00:00
datasources/pipeline	Updated from SnakeYAML 1.6 to 1.7.	2010-09-22 19:47:49 +00:00
gatk	Added - a tool to fix reference bases of a VCF. The OMNI had a couple of sites with incorrect reference bases (look to be legacy from other chips), and a few more that had ref and alt flipped. GAP should probably take care of it, but since I need results by monday, I'm doing it.	2010-10-17 03:18:01 +00:00
oneoffprojects/walkers	The tribble indexes are now updated with correct sequence lengths for each contig they have in their sequence dictionary. Also clean-up in the RMD track builder.	2010-09-21 18:21:22 +00:00
playground/gatk/walkers	Recent changes to the build system make the build system complain loudly about	2010-09-24 22:09:12 +00:00
utils	High performance version of standard vcf writer. New general static Tribble class for common constants, including general .idx constant and functions to get standard index name for a given file.	2010-10-08 19:53:21 +00:00
BaseTest.java	Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality.	2010-10-06 18:29:56 +00:00
WalkerTest.java	High performance version of standard vcf writer. New general static Tribble class for common constants, including general .idx constant and functions to get standard index name for a given file.	2010-10-08 19:53:21 +00:00