previous method broke the SAM/BAM definition and didn't properly read paired-end data aligned with bowtie. Taking the rightmost read also isn't possible when only one read is aligned (so it unnecessarily discards a lot of data)
updated SAMParser, too
saved local progress
Merge branch 'master' of git://github.com/taoliu/MACS
Implemented BAMPEParser for proper paired-end data -- uses fragment
midpoints and skips modeling step for peak calling
finalized funtionality to call peaks directly from true data
added --call-summits flag to call subpeaks within each enriched region
(if --call-summits is excluded, MACS will use old method). new method
uses 3-pass approach: look for local maxima above mean, use only one
coordinate per begraph entry, and require a dip to 60% of taller signal
between subpeaks. handles doublets well, sometimes misses small
subpeaks.

modified some output for better compatibility with genome browser, etc
rewrote cPeakIO with python v3 print function so there's no need for
separate print/write methods
Disable filtering of duplicates by default in BAMPE mode
added useful tracklines by default
	for bedgraphs and BED files (peaks/summits)
added --no-trackline option to disable tracklines
added name column (last) to xls file

matched up all names between xls and BED files for consistency
added useful tracklines by default
	for bedgraphs and BED files (peaks/summits)
added --no-trackline option to disable tracklines
added name column (last) to xls file

matched up all names between xls and BED files for consistency
Merge branch 'master' of git@github.com:benjschiller/MACS.git
added missing imports
added missing keyword arguments
more missing keyword arguments
more missing keyword arguments
fixed main script. removed tag filtering from BAMPE mode
added assert statement to enforce pvalues are numbers
Merge branch 'master' of git://github.com/taoliu/MACS

Conflicts:
	MACS2/IO/cParser.pyx
	MACS2/IO/cScoreTrack.pyx
	bin/macs2
Merge branch 'master' of github.com:benjschiller/MACS
added missing newline in BED tracklines
fixed trackline output in no control case