Convert "properly read" constants to command line parameters

[gdgib-roche]

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: controls how to calculate low and high boundaries for proper pairs. Low and high boundaries is calculated : F(Q1, Q2, Q3, mapping_bound_mem, max_stddev_mem) where Q2 is median insert size, Q1 and Q3 are lower and higher quartile (also see max_stddev_mem).
• --max_stddev_mem: controls how to calculate low and high boundaries for proper pairs. Low and high boundaries is calculated : F(Q1, Q2, Q3, mapping_bound_mem, max_stddev_mem) where Q2 is median insert size, Q1 and Q3 are lower and higher quartile (also see mapping_bound_mem).

[gdgib-roche]

Anyone got a few minutes to review? I'll resolve conflicts if there's any chance this will be merged.