Various warning fixes

Compiling with the version of clang that comes with OS X Mavericks produces a number of warnings, many of which pertain to small issues in header files and so are repeated over and over during a full build.  These suggested changes fix those in headers and a few others.  There is also a small test case fix.

The `using` declarations in 78b8caf94394d7c3292f9c5a737bc19bee5ded0c silence the warning and make all the `initFromFile` and `print` methods available, including those from the base class.  The latter may or may not be desired, so this might not be the right fix.

b802a489a2dc5c51a6011194a971c206b16e1073 affects bamtools files, and is also jmarshall/bamtools@f8d2c31b606df8e85b6cb21a5dc8bd9fd9ff4ade in pull request pezmaster31/bamtools#93.  So you might want to see what the bamtools folks do with this one before applying it to bedtools.