Fixed problem with negative mapping distances bedtools

This was a problem in a Bam I generated, using BWA where the read had a start position == 0.

HWUSI-EAS1599_0001:8:116:8882:17709#0   113     chr10   0       25      75M     chr1    36082549        0       CCTTAAACCCTAAACCCTAATCCCTAAACCCTAAACCCTAAACCCTTAAGCCTAAACCCTAAACCC.

Created downstream problems when calculating coverage as it left me with summaries with regions of the genome having -1 reads mapping within.