Updates to work with samtools Version: 0.1.16 (r963:234) bwa Version: 0.6.1-r104, bedtools v2.16.2
Updates to work with samtools Version: 0.1.16 (r963:234) bwa Version: 0.6.1-r104, bedtools v2.16.2

AlastairKerr/Marston2013,AlastairKerr/Marston2013,AlastairKerr/Marston2013