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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engine	Update licenses for new PbsEngine* classes	2013-07-01 15:50:20 -04:00
extensions	Updated Full Processing Pipeline	2013-08-13 23:35:32 -04:00
function	Added a QFunction.jobLocalDir for optionally tracking a node local directory that may have faster intermediate storage, with SGF ensuring that if the directory happens to be on the same machine that it get's a clone specific sub-directory to avoid collisions.	2013-01-25 14:28:04 -05:00
library	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
util	Adaptations to accomodate Tribble API changes, comprising mostly of the following.	2013-08-19 15:52:47 -04:00
QCommandLine.scala	Message "script failed" moved to the correct place in the code	2013-02-04 15:37:23 -05:00
QCommandPlugin.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
QException.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
QScript.scala	Update QScript.scala	2013-08-02 14:09:26 -04:00
QScriptManager.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
QSettings.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00