`samtools mpileup` is being replaced with `bcftools`

[andersgs]

This can be fixed with the following changes to lines 346 and 348:

run_command(
    [args.bcftools_location + 'bcftools', 'mpileup', '-q', str(args.phred), '-B', '-f', 'temp_reference.fasta',
    '-t', args.ref_id + '.bed', bam, '-Ou','-o', bam[:-4] + '.output', '-I']) # detect SNPs

Basically, remove -u and -g and use Ou, and replace -l with -t.

A.