Khalid Shakir 2ef456d51a 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. ... Changed ReflectionUtils.getGenericTypes' order of looking for @ClassType since the primitive generic wasn't completely erased, only changed to Object which is incorrect. More fixes to @Arguments labeled as java.io.File via incorrect @Input annotation. Put in a default undocumented implementation of @Argument doc() to match the one added to @Input.		2012-10-19 13:20:29 -04:00
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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	Update from dbsnp135 to dbsnp137.	2012-08-31 14:06:29 -04:00
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