samtools/htsjdk — pull request #21 by BeatWolf (2014-05-24 10:12:06+00:00)
Title: Binning index context speedup

BinningIndexContent.getChunksOverlapping showed up as a major bottleneck when profiling one of my test applications. I noticed that it iterates over a lot of Bins, to only look at a handfull of them in the end (for example 5 bins where marked as true in overlappingBins but there where over 10'000 bins to loop through).

This patch makes the function only look at the Bins that are actually interesting. I got a 40% speed improvement in my testcase.