Whitespace cleanup Yak shaving.
Added clipper as a caller for RNA-seq peak data.

Useful for CLIP-seq, IMPACT-seq, among others, anything with
thin peaks on transcripts without the phantom peak to call like
in CHIP-seq experiments. Not as good for PAR-Clip because it
doesn't take the nucleotide change into account.

Also added the ability to process BAM files instead of tagalign.