lcolladotor/derfinder — pull request #24 by lcolladotor (2014-06-05 20:10:09+00:00)
Title: Memory improvements to all parallel functions, new methods for F-stats calculation, recommended fullCoverage() and improved regionMatrix()

* Improved getRegionCoverage()
* regionMatrix() changed and can now take several types of input. Check news for version 0.0.61 for more details.
* Major change: dropped parallel::mclapply() in favor of BiocParallel::bplapply() using BiocParallel::SnowParam(). This lead to a considerable reduction in memory needed for all the functions that use multiple cores. Check news for version 0.0.62 for more details.
* fstats.apply() now has 3 different methods for calculating the F-statistics with the new default using the Matrix package. It's faster and less memory intensive than the default one with real data sets (not with tiny example ones). There is also a method that does everything at the Rle level but grows slow fast as the number of samples increases. Check news for version 0.0.63 for more details.
* fullCoverage() is now the recommended function for loading coverage instead of using a single job per chr with loadCoverage() or lapply(loadCoverage). Check news for version 0.0.64 for details.