David Roazen 1296dd41be Removing the legacy -L "interval1;interval2" syntax ... This syntax predates the ability to have multiple -L arguments, is inconsistent with the syntax of all other GATK arguments, requires quoting to avoid interpretation by the shell, and was causing problems in Queue. A UserException is now thrown if someone tries to use this syntax.		2011-11-21 13:18:53 -05:00
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IntervalMergingRule.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
IntervalSetRule.java	Fixing docs and adding GATKdocs for the new interval functionality	2011-10-26 22:14:43 -04:00
IntervalUtils.java	Removing the legacy -L "interval1;interval2" syntax	2011-11-21 13:18:53 -05:00
OverlappingIntervalIterator.java	Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.	2011-07-17 20:29:58 -04:00