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

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changed logo.
	5. Revised the usage statement.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changed logo.
	5. Revised the usage statement.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changes logo.
	5. Revised the usage statement.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changes logo.
	5. Updated bedFile.cpp's loadBedIntoMapBin to support stdin.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changes logo.
	5. Updated bedFile.cpp's loadBedIntoMapNoBin.  Bug in stdin logic.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic

	1. Added GPLv2 license to entire distribution
	2. Added GPL headers to intersect and window
	3. Added new stdin logic to windowBed

	1. Got parseGffLine working
	2. Added GFF support to the reportBed* methods.
	3. Cleaned up the stdin / parsing logic and centralized it within bedFile.cpp.
	This removes some of the complexity from each of the tools and tidies the codebase
	overall.