adding new files for computing bigwig correlation. The code is not yet complete
functional bigwig correlate
Changed behavior of bigwigCorrelate and deeptools/getScorePerBigWigBin.py to use consecutive bins. Also updated the command line help. An issue remains with the max and max/2 options for processor usage.
Deleted -f option in bin/bigwigCorrelate. (I used it for --filterPercentile, which overlaps with the option for fragment length in other deeptools). Quick note: max and max/2 seems to work, though my negative claim in my last commit.
Changed deeptools/countReadsPerBin.py to use the entire genome (last bin might be smaller) and consecutive bins (stepSize=binLength).
bamCorrelate now uses the basename (and not the full path) of the input files as lables by default.
Added the filter option --filterPercentile to bamCorrelate. filterPercentile is used instead of the fixed 99.9 value before to remove extreme outliers.
Minor changes to documentation of command line options; lots of indentation correction in the code.
In numberOfSamples is given and smaller than the number of bins, random bins are discarded
Removed '--numberOfSamples' option from bamCorrelate and bigwigCorrelate, because it does not work (as one would expect) by design.
Merge branch 'master' of https://github.com/fidelram/deepTools into bigwigCorrelate
added option for distance between bins, dropped option numberOfSamples.
merge
changed order of options, now spearman is first
revert change in countReadsPerBin in which a last short bin was now being included but this may cause problems with other dependencies
added options to galaxy wrapper
NEW dropped the option to filter outliers using the percentile method. Instead a more powerful method to detect outliers is now used. This method is based on the median absolute deviation.
new version for branch
updated tool description
fixed typo