-wa allows the original A entry to be written for each overlap with B.

	1. Changed intersectMain.cpp, complementMain.cpp and mergeMain.cpp to
	   include information on how to run using stdin.

	1.  Changed BedFile::loadBedFileIntoMapNoBin() to allow either "" or "stdin".
	2.  Consequently, this allows mergeBed to accept stdin as well.

	1.  Changed the cout statements for the last entries for a chromosome.
	2.  I had forgotten to report the number of merged entries when -n is requested.
	3.  I also fixed a bug that occassionally caused the last entry for a chromosome
	    to report the chrom twice in the output.

	Rather self-explanatory.  Affects *Main.cpp files.
	Also affects the bedFile.cpp file.
		All of the BED entry checks now write to stderr.

	1.  Fixed a bug that caused genomeCoverageBed to crash on Linux systems.
	2.  Refined the algorithm to use less memory.  It's a bit slower now, but uses 1/3 the memory.
	3.  Changed the logic for computing depth to conform to the UCSC coordinate system.

There will no longer be local copies of the binaries in each of
the respective src/* directories

	Changed the include from graphBed.h to coverageBed.h
coverageMain.cpp:
        Changed the include from graphBed.h to coverageBed.h

Changed sortBed to allow input from stdin.