Read name parsing and optical duplicate detection option

See commit messages.

At the very least the first commit ("Correctly parse newer...") should be merged, as it is a bug fix.

The other two are small features, not bug fixes.

Related to [this thread on samtools-help](http://sourceforge.net/p/samtools/mailman/samtools-help/thread/56CFC6EA-B9F2-436B-8506-B7F6C22C3DD4%40uw.edu/#msg32741916).