drop unused argument, expanded docstring
added extendPairedEnds, minMappingQuality and ignoreDuplicates to getNumReadsPerBin. Added the proper tests and modified the test bam files which didn't have mapping quality
fixed usage, instead of -method it should be --corMethod. Moved command line arguments found in parserCommon to the bamCorrelate file and dropped the smoothLengh parameter.  Most changes are related to pep8 cleanup
added support for bamFingerprint to minMappingQuality, ignoreDuplicates, and doNotExtendPairedEnds. Moved common options for bamCorrelate and bamFingerprint to parserCommon
Merge branch 'master' of https://github.com/fidelram/deepTools into multi_bigwig_heatmapper
colormaps with more than 2 colors were not displaying properly in bamCorrelate
replaced hardcoded value
Changed message in heatmapper.py for duplicated regions
Fix for the case when an unmapped paired read is given the genomic positionof the mate. I added a filter to only consider reads flaged as mapped.
Fix doctest to pass under the new filtering conditions
Changed os.system call by subprocess.check_call to catch any problems while running shell commands
Improve explanation of scaling factors for the normalizeTo1x option
Merge branch 'master' of https://github.com/fidelram/deepTools into multi_bigwig_heatmapper
documentation fix
Merge branch 'master' of https://github.com/fidelram/deepTools into multi_bigwig_heatmapper
restructured the way the matrices are saved, loaded and internally accesed. The new methods allow a cleaner plotting using gridSpec. Currently kmeans and sorting work but saving the BED regions or the matrices does not work. Profiler now can plot either by groups or by samples (sample is each bigwig file given). Heatmapper now plot each sample indidually but the in the layout some large white space is added.