Fix minor bugs and add support for MiSeq.

Here're my patches for fixing two minor bugs and new support for .locs coordinate format produced by MiSeq.

512c211 - Fix compilation in modern Linux linkers, which requires for list of libraries to be specified later than their consumers.
5483042 - Print quality scores for compressed formats of FASTQ, too.
de92f59 - Add support for .locs format for MiSeq.