Louis Bergelson b32ad99d3f Changing from scala 2.9.2 to 2.10.2. ... --modified ivy dependencies --modified scala classpath in build.xml to include scala-reflect --changed imports to point to the new scala scala.reflect.internal.util --set the bootclasspath in QScriptManager as well as the classpath variable. --removing Set[File] <-> Set[String] conversions ----Set is invariant now and the conversions broke --removing unit tests for Set[File] <-> Set[String] conversions		2013-09-23 12:42:22 -04:00
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R	Something changed with the ggtitle syntax in the latest version of ggplot2.	2013-08-14 14:40:03 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	…
doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Provide close methods to clean up resources used while creating AlignmentContexts from BAM file regions. Allows utilization of CoveredLocusView via the API	2013-09-10 15:32:54 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -05:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Changing from scala 2.9.2 to 2.10.2.	2013-09-23 12:42:22 -04:00
testdata	Walker to create a fastq file from an interval list	2013-06-29 11:24:16 -04:00