Fixed a stupid buig in the peak calling code
Fixed some bugs in the peak calling stand alone script. Changed the output to narrowPeak format.
Added a maximum peak size option
Added an ATAC seq option for bam2wig
Added code which allows peaks to be called without a refernce genome
moved find_coverage intot he gene object
Did some refactoring, cleaned up the peaks.py config option handling
Fixed a couple of small bugs
Added code to try and be smarter about merging regions, but then commented it out because I dont think the approach is ideal
Fixed a small argument parsing bug
Fixed a compatability bug for CAGE bams
Added in max and min fragment length configuration options
Refactored the read mapping posterior probability code
Cleaned up merge