update bamqc error-rate version selection

test for bwa mem:
    $name eq 'bwamem' # do not want
    $name =~ /^bwamem/ # much better (matches bwamem-stream)
import fixups

removing some unused imports.
add bedtools 2.17.0 to valid versions

This is already installed, we just didn't have it in the version hash.
Some other minor module cleanup (whitespace/errmsgs) too.
add bam input to gmt bwa run-mem

this lets us stream from bam -> fastq rather than dumping fastqs to /tmp