Limit coordinate range for requests

[kautto]

Currently, when requesting reads from the input BAM files, a 5 base pair padding is added to the range of coordinates. This can result in a negative coordinate value (e.g. with a start coordinate of 1, the request would start at -4). This will cause an error with Pysam that results in the program crashing. The range of the request coordinates needs to be limited so that only valid (> 0) values are used in requests.