Eric Banks f82a7c3f4c Updating variant jar. ... The update contains: 1. documentation changes for VariantContext and Allele (which used to discuss the now obsolete null allele) 2. better error messages for VCFs containing complex rearrangements with breakends 3. instead of failing badly on format field lists with '.'s, just ignore them Also, there is a trivial change to use a more efficient method to remove a bunch of attributes from a VC. Delivers PT#s 59675378, 59496612, and 60524016.		2013-12-31 22:48:29 -05:00
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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, sam-jdk, tribble, and variant jars to 1.104.1628	2013-12-05 12:45:32 -05:00
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, sam-jdk, tribble, and variant jars to 1.104.1628	2013-12-05 12:45:32 -05:00
org.broadinstitute	Updating variant jar.	2013-12-31 22:48:29 -05:00