hhv3 requires new coverage outputs

Pindel annotation bug fix, probe coverage updates, pindel parsing for…

… bwamem/bbmerge

added GRIDSS annotations; fixed bug in Pindel analysis; report abs fo…

…r pindel/breakdancer size

change pindel insertion position reporting to start-(start+1)

reporting absolute values for variant size from breakdancer and pindel

update coverage metrics to create intervals correctly

update annotsv_summary to include lenth, breakdancer to process chr p…

…refix correctly and pindel to provide exon/intron ranges

new parsing scripts for annotsv, breakdancer and pindel

add summarize_assay qc script

use internal or external mutalyzer