change surject to use filtered bam.  run vg filter before pileup to save intermediary but at cost of speed
change surject to use filtered bam.  run vg filter before pileup to save intermediary but at cost of speed

adamnovak/hgvm-graph-bakeoff-evaluations,glennhickey/hgvm-graph-bakeoff-evalutations,glennhickey/hgvm-graph-bakeoff-evaluations,adamnovak/hgvm-graph-bakeoff-evaluations,glennhickey/hgvm-graph-bakeoff-evalutations,glennhickey/hgvm-graph-bakeoff-evaluations,BD2KGenomics/hgvm-graph-bakeoff-evalutations,adamnovak/hgvm-graph-bakeoff-evalutations,BD2KGenomics/hgvm-graph-bakeoff-evalutations,BD2KGenomics/hgvm-graph-bakeoff-evalutations,glennhickey/hgvm-graph-bakeoff-evalutations,adamnovak/hgvm-graph-bakeoff-evalutations,adamnovak/hgvm-graph-bakeoff-evaluations,glennhickey/hgvm-graph-bakeoff-evaluations,adamnovak/hgvm-graph-bakeoff-evalutations