Ability to add flat files for options and skip complex regions.

[Shawn Rynearson]

Considering a few WHAM-GRAPHING options:

 Required:
          -f - <STRING> - A sorted and indexed bam file or a list
                          of bams: a.bam,b.bam,...
 Optional:
          -e - <STRING> - Comma sep. list of seqids to skip [false].
          -r - <STRING> - Region in format: seqid:start-end [whole genome]

1. It would be helpful if you could supply flat files for all three of these options. As opposed to supplying long lists of comma separated files.
   ./WHAM-GRAPHING -f reference.fasta -f bam_files.txt -r regions.bed.

This would improve not only ease of use, but allow better cohort and targeted gene analysis.

1. It would be nice to have the ability to tell WHAM regions to downsample or skip altogether.
   ./WHAM-GRAPHING -f reference.fasta -f bam_files.txt --skip complexity_regions.bed.
2. Also a bit more clarity on how the -r option works in regards to calling SV and genotyping.