Mark DePristo eb60235dcd Working version of incremental active region traversals ... -- The incremental version now processes active regions as soon as they are ready to be processed, instead of waiting until the end of the shard as in the previous version. This means that ART walkers will now take much less memory than previously. On chr20 of NA12878 the majority of regions are processed with as few as 500 reads in memory. Over the whole chr20 only 5K reads were ever held in ART at one time. -- Fixed bug in the way active regions worked with shard boundaries. The new implementation no longer see shard boundaries in any meaningful way, and that uncovered a problem that active regions were always being closed across shard boundaries. This behavior was actually encoded in the unit tests, so those needed to be updated as well. -- Changed the way that preset regions work in ART. The new contract ensures that you get exactly the regions you requested. the isActive function is still called, but its result has no impact on the regions. With this functionality is should be possible to use the HC as a generic assembly by forcing it to operate over very large regions -- Added a few misc. useful functions to IncrementalActivityProfile		2013-01-23 13:46:00 -05:00
..
sting	Working version of incremental active region traversals	2013-01-23 13:46:00 -05:00
variant	Merge branch 'master' of github.com:broadinstitute/gsa-unstable	2013-01-16 14:59:11 -05:00