* The value of this element (default true) determines whether Queue will explicitly run this walker over unmapped reads
* This patch fixes a runtime error when FindCoveredIntervals was used with Queue
* PT 81777160
Changed tests and scripts to use gatkdir full path instead of relative testdata/qscripts symbolic links.
Although symlinks not created, left the symlink deletion script execution with a comment about future removal.
Re-enabled example UG pipeline queue test.
Replaced all hardcoded strings of {public,private}/testdata with BaseTest variables.
Refactored temp list creation method from ListFileUtilsUnitTest to BaseTest.createTempListFile.
Removed list files with hardcoded paths, now using createTempListFile instead with private test dir variable.
Geraldine Van der Auwera
Laura Gauthier
Phillip Dexheimer
Khalid Shakir