Greg Gibeling

Convert "properly read" constants to command line parameters

1

3 new parameters to control how bwa mem tags reads as "properly mapped": * `--outlier_bound_mem`: controls how to calculate low and high boundaries for computing mean and std.dev. * `--mapping_bound_mem`:...

ToolInformation - Equals, HashCode, and multi-tool parsing fixes w/tests

2

1. The new ToolInformation class did not have equals & hashCode methods, which prevented equality checks during downstream unit testing 2. The custom deserializer for ToolInformation did not correctly handle...