Mauricio Carneiro c210b7cde4 Merge GATK repo into CMI-GATK ... Bringing in the following relevant changes: * Fixes the indel realigner N-Way out null pointer exception DEV-10 * Optimizations to ReduceReads that bring the run time to 1/3rd. Conflicts: protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java DEV-10 #resolve #time 2m		2012-10-23 10:59:11 -04:00
..
engine	Moved the class field caching from QScript to a ClassFieldCache utility.	2012-10-16 18:49:31 -04:00
extensions	a) Resolve [#DEV-56] - test data with indels in new directory private/testdata/CMITestData/. b) Skeleton (not yet working) of fastq-BAM unit test, c) misc bug fixes for QC functions to work (not done yet)	2012-10-22 19:59:15 -04:00
function	Moved the class field caching from QScript to a ClassFieldCache utility.	2012-10-16 18:49:31 -04:00
library	Fix edge case for very small VCFs	2012-01-19 00:51:28 -05:00
util	Merge GATK repo into CMI-GATK	2012-10-23 10:59:11 -04:00
QCommandLine.scala	Added another utility that can convert to RemoteFiles.	2012-10-17 20:00:03 -04:00
QCommandPlugin.scala	Added another utility that can convert to RemoteFiles.	2012-10-17 20:00:03 -04:00
QException.scala	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
QScript.scala	Added another utility that can convert to RemoteFiles.	2012-10-17 20:00:03 -04:00
QScriptManager.scala	Fixed package error and a few deprecated scala warnings.	2012-10-15 15:29:40 -04:00
QSettings.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