new script to replace Homer annotatePeaks.pl
Add index bam to function

Add index bam after get sorted bam.
Update inputProcess.py
Update SAMFilter.py
Update SAMFilter.py
wrapped barcodeRemoval main into a seperate class and run function
refactored the code in a more object oriented fashion
there should be no issue with running the from before
needs testing
Added file integrity check
Update inputProcess.py
Change to Eric structure
Change to Eric structure

Put every functions into methods of class
Fix typo
converted all tabs to spaces
started developing the wrapper for pipeclip
modified the scripts for a parameter passing main, and changed the
scripts to directly write produced fiels instead of piping stdout to a
file
refined the wrapper script
modified the wrapper to accept named command line arguments
modified mergeReads to accept a parameter for the output file
modifed pipeclip wrapper to more accurately represent the original bash script
and idention error caused for an ambigous algorithm
Removed "rehead"

Since Samtools functions are included within script, there is no need to reheader an output BAM. So the output files will not contain "rehead" in their filenames.