v0.0.65 Re-organized fstats.apply()
v0.0.66 -- shipped fstats.apply() to derfinderHelper and the three plotting functions to derfinderPlot. Fixed the namespace for recent changes in IRanges and S4Vectors. Fixed links to functions now residing in other packages. Still running some tests to try to reduce the loading time for derfinderHelper::fstats.apply() as it currently can dominate the time for some small chrs with small chunks (like chrY).
v0.0.67 -- Now preprocessCoverage() has a toMatrix argument which can reduce time when using lowMemDir and the 'Matrix' method for derfinderHelper::fstats.apply()
v0.0.68 -- minor tweak to filterData() which could be influential in large data sets
v0.0.69 -- testing using GenomicFiles for loadCoverage() and fullCoverage(). I expect it to be much slower, but I am curious to see how much RAM it needs
Added more control in fullCoverage() for the number of cores used in loadCoverage()
Upgraded R from 3.1.x to 3.1.1 that was recently released and will be using this version to check now. Fixed a link in the docs now that GenomicFeatures?TranscriptDb is called GenomicFeatures?TxDb. Check currently takes 268 secs
Added an example of how to export the coverage to BigWig format and compared the results of using loadCoverage(inputType='bam') versus loadCoverage(inputType='bigWig'). The BAM import uses integer-Rle while the BigWig import uses numeric-Rle.
Fixes #26
v0.0.70 -- Added underscore aliases for all the functions so users can use their preferred version. Doing so doesn't increase the time in R CMD check
Renamed makeBamList() as rawFiles()
Renamed the .R file
v0.0.71 -- Added functions for exporting BigWig files
Added examples for coerceGR(), createBw() and createBwSample(). Fixed a couple of bugs in these functions.
Updated to work with the latest BioC pkgs
Fix verbose messages
Added travis -- still learning how to use it
Using the version @siddharthab changed to allow BioC-devel -- Still testing
Added derfinderHelper github install -- added status image (testing this) -- updated README
Test new version of travis-tool.sh with derfinderHelper 0.0.5