Have STAR set the read group tags.

This saves a call out to AddOrReplaceReadGroups. There is
an issue with it, though, that it creates a malformed header.
https://groups.google.com/d/msg/rna-star/xxE4cUnafJQ/EUsgYId-dB8J

A fix is in place to handle it for now and can be removed
if/when the bug is fixed upstream.

Added reheadering function for BAM files.
Use AlienTrimmer instead of cutadapt.

AlienTrimmer is much faster the way we are using it, at
least 10x faster. We do less trimming this way, and will
lose some reads but taking hours and hours to trim the
reads perfectly isn't worth the effort to recover a small
number of reads.
Fix for annotation for GTF files without standard fields.

This just bails out annotating the file.