Mark DePristo d5dd3b23db Rev picard to get optimized tribble feature reads ... -- The previous version of TribbleIndexedFeatureReader.query() would open a RandomAccessFile each time the GATK crossed a shard boundary. When running with -L wex.intervals (or any time there were lots of intervals) we'd be opening and closing enormous numbers of files, radically slowing down the GATK. With these patched versions of Tribble we see something like the following performance improvements: SelectVariants with -L wex.intervals on my local machine against non-local file pre-patch => 3 hours post-patch => 30 seconds		2013-08-02 10:31:36 -04:00
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com.google.code.caliper	Killed sonatype repository; it's failed me too many times at this point.	2011-06-09 16:07:02 +00:00
com.google.code.cofoja	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00
edu.mit.broad	Rev picard, sam-jdk, tribble, and variant jars to version 1.90.1442	2013-04-25 14:05:24 -04:00
gov.nist	Adding Jama for Ryan.	2010-04-27 14:30:36 +00:00
net.sf	Rev picard to get optimized tribble feature reads	2013-08-02 10:31:36 -04:00
net.sf.gridscheduler	Switched GridEngine from looking from environment variable to using embedded jar.	2011-07-05 21:59:00 -04:00
net.sf.snpeff	SnpEff 2.0.5 support. Re-enabled SnpEff in the HybridSelectionPipeline.	2012-01-03 15:18:36 -05:00
org.broad	Rev picard to get optimized tribble feature reads	2013-08-02 10:31:36 -04:00
org.broadinstitute	Rev picard to get optimized tribble feature reads	2013-08-02 10:31:36 -04:00