Michael McCowan c3a933ce84 Adaptations to accomodate Tribble API changes, comprising mostly of the following. ... * Refactoring implementations of readHeader(LineReader) -> readActualHeader(LineIterator), including nullary implementations where applicable. * Galvanizing fo generic types. * Test fixups, mostly to pass around LineIterators instead of LineReaders. * New rev of tribble, which incorporates a fix that addresses a problem with TribbleIndexedFeatureReader reading a header twice in some instances. * New rev of sam, to make AbstractIterator visible (was moved from picard -> sam in Tribble API refactor).		2013-08-19 15:52:47 -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	Adaptations to accomodate Tribble API changes, comprising mostly of the following.	2013-08-19 15:52:47 -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	Adaptations to accomodate Tribble API changes, comprising mostly of the following.	2013-08-19 15:52:47 -04:00
org.broadinstitute	Rev'ing picard, tribble, and variant jars.	2013-08-16 00:16:31 -04:00