gatk-3.8/public/java/src/org/broadinstitute/sting
David Roazen 5baf906c28 Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists
-The algorithm for finding the intersection of two sets of intervals
 relies on the sortedness of the intervals within each set, but the engine
 was not sorting the intervals before attempting to find the intersection.

-The result was that if one or both interval lists was unsorted / lexicographically
 sorted, we would often fail to find the intersection correctly.

-Now the IntervalBinding sorts all sets of intervals before returning them,
 solving the problem.

-Added an integration test for this case.

GSA-909 #resolve
2013-04-02 14:01:52 -04:00
..
alignment Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
commandline Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists 2013-04-02 14:01:52 -04:00
gatk Merge pull request #135 from broadinstitute/mc_pgtag_fix 2013-03-31 11:36:40 -07:00
jna Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
queue change the default VCFs gatherer of the GATK (not just the UG) 2013-01-18 15:03:12 -05:00
tools Created ListAnnotations utility (extends CommandLineProgram) 2013-03-20 06:15:27 -04:00
utils Fixing @PG tag uniqueness issue 2013-03-30 20:31:33 -04:00