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