consistency with biometrics package

[ionox0]

As @murphycj2 has done in the biometrics package, lets make this package use pysamstats (which really just calls to pysam) in the same way:

• Ensure stepper is not eliminating duplicate reads (use nofilter?) Include duplicate reads for pileup alimanfoo/pysamstats#91
• Figure out a way to avoid double-counting overlapping reads (ignore_overlap param does not get passed to pysam... Counting overlapping read-pairs alimanfoo/pysamstats#98)
• Set min_mapping_quality truncate and max_depth defaults to same value as biometrics (and ensure they are exposed as parameters)
• Can we be consistent with min_base_quality or do the noise and fingerprinting require different values for this to work?
• We might still want to consider the possibility of combining these two calculations into the same package

[rhshah]

Did you finish updating any of this @ionox0

[ionox0]

• default min_base_quality in both packages is set to 1
• default min_mapping_quality in both packages is set to 1
• stepper being used is nofilter in both packages
• max_depth being used is 30000 in both packages

I'll make another change to expose these parameters in case we don't want do use defaults

For the ignore_overlaps issue, I'm not sure how to supply that parameter to pysam without making a PR to pysamstats, but I could do that if it's a good option

[ionox0]

Correction on that last point, actually by setting the min_base_quality to 1, we are effectively avoiding double-counting overlapping reads, because pysam sets the one with lower base quality to 0, and then we filter it out:

alimanfoo/pysamstats#98 (comment)

[ionox0]

I've added max_depth as a parameter as part of this PR #15 , so all parameters are now exposed