add chroms for speedseq.config and README cnvnator chroms dir
lumpy has better insert distribution construction
updated lumpy-sv
added read-depth annotation to speedseq sv (cnvnator now does 1kb bins as well)
VEP annotation of SVs
fixed a verbose comment
reinstated gemini to python install
properly updates the VCF header after parallel genotyping (previously this would cause annotate_rd to fail)
fixed critical error in annotate_rd, where variants of neg size would be skipped by cnvnator and cause a shift for the rest of the CN annotations
Makefile now checks for ROOT and only installs CNVNator if it detects it
fixed a bug that wouldn't source VEP in speedseq somatic
updated freebayes
fixed critical bug that caused part of vcf header to be left out
added bwa
use bwa version 0.7.8
moved bwa to speedseq repo
remove manual install of bwa from readme