be45edeff2
-- Active regions are created as normal, but they are split and trimmed to the engine intervals when added to the traversal, if there are intervals present. -- UnitTests for ActiveRegion.splitAndTrimToIntervals -- GenomeLocSortedSet.getOverlapping uses binary search to efficiently in ~ log N time find overlapping intervals -- UnitTesting overlap function in GenomeLocSortedSet -- Discovered fundamental implementation bug in that adding genome locs out of order (elements on 20 then on 19) produces an invalid GenomeLocSortedSet. Created a JIRA to address this: https://jira.broadinstitute.org/browse/GSA-775 -- Constructor that takes a collection of genome locs now sorts its input and merges overlapping intervals -- Added docs for the constructors in GLSS -- Update HaplotypeCaller MD5s, which change because ActiveRegions are now restricted to the engine intervals, which changes slightly the regions in the tests and so the reads in the regions, and thus the md5s -- GenomeAnalysisEngineUnitTest needs to provide non-null genome loc parser |
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