add gmt bwa run-mem

A command to map fastqs to coordinate sorted bam files with bwa mem.
Might be useful to be more specific with the unknown cases.

For example:
`return "$unknown: missing $path" unless -s $path;`
`return "$unknown: $path had too many lines:\n" . (join "\n", @lines) unless @lines == 1;`
`return "$unknown: $path had wrong number of commands: @status" unless @status == @commands;`

Or something like that.