1. atoi fails in parseLine when start = 0.  Changed to strtol.
	2. modified parseBedLine and parseGffLine to do better sanity checking.

	1. pairToBed had a bug in the way it parsed -a
	2. extraneous tr1/unordered_map include in bedfile.h causes compile issues on some machines.

	There was a problem with the way args with a value were being parsed.

	1. Fixed bugs in parsing command line booleans in fastaFromBed and maskFastaFromBed
	2. Added tabular output to fastaFromBed

extract beyond the length of a chromosome.

	1. If intrachromosomal, choose the leftmost end.
	2. Else, choose the first mate.

	- also added map quality as score in pairToBed