Mark DePristo a1093ad230 Optimization for ActiveRegion.removeAll ... -- Previous version took a Collection<GATKSAMRecord> to remove, and called ArrayList.removeAll() on this collection to remove reads from the ActiveRegion. This can be very slow when there are lots of reads, as ArrayList.removeAll ultimately calls indexOf() that searches through the list calling equals() on each element. New version takes a set, and uses an iterator on the list to remove() from the iterator any read that is in the set. Given that we were already iterating over the list of reads to update the read span, this algorithm is actually simpler and faster than the previous one. -- Update HaplotypeCaller filterReadsInRegion to use a Set not a List. -- Expanded the unit tests a bit for ActiveRegion.removeAll		2013-05-21 16:18:57 -04:00
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java	Optimization for ActiveRegion.removeAll	2013-05-21 16:18:57 -04:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00