Eric Banks 18728ec5bd Updates to the bundle script: ... 1. Add the symbolic 'current' link for the new bundle dir 2. Don't gzip and copy .out files 3. Don't call chr20 SNPs on the example BAM because it's now just a few reads on chr1		2012-12-18 11:16:42 -05:00
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CNV	Fixed fragment handling in DepthOfCoverage	2012-11-21 16:01:10 -05:00
examples	RetryMemoryLimit now works with Scatter/Gather.	2012-10-09 21:51:03 -04:00
lib	Mostly small changes to my own scala scripts: .vcf.gz compatibility for output files, smarter beagle generation, simple script to scatter-gather combine variants. Whole genome indel calling now uses the gold standard indel set.	2012-02-22 17:20:04 -05:00
DataProcessingPipeline.scala	Fixed null checkes in ArgumentTypeDescriptor due to ArgumentMatchValue updates.	2012-10-18 16:57:15 -04:00
GATKResourcesBundle.scala	Updates to the bundle script:	2012-12-18 11:16:42 -05:00
MethodsDevelopmentCallingPipeline.scala	Turning off PHONE HOME option in the MDCP	2012-01-27 11:13:30 -05:00
PacbioProcessingPipeline.scala	Added explicit @ClassType annotations to @Argument for Option[Int] or Option[Double] since scala seems to change the reflected type to Option[Object] on some systems.	2012-10-19 13:20:29 -04:00