Count ambiguities

[lskatz]

Hi @chienchi,
I hope pull requests are welcome. I have been using amplicov for a couple of weeks now and wanted to add a new line denoting number of ambiguities. In this context, I defined ambiguities as places in the bam file that have < 10x coverage.

[codecov]

Codecov Report

Merging #1 (5caa0fb) into master (21d0578) will increase coverage by 2.04%.
The diff coverage is 87.09%.

@@            Coverage Diff             @@
##           master       #1      +/-   ##
==========================================
+ Coverage   71.58%   73.63%   +2.04%     
==========================================
  Files           1        1              
  Lines         183      201      +18     
==========================================
+ Hits          131      148      +17     
- Misses         52       53       +1     

Impacted Files	Coverage Δ
amplicov/amplicov	73.63% <87.09%> (+2.04%)	⬆️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 21d0578...5caa0fb. Read the comment docs.

[chienchi]

Yes, thanks @lskatz for contributing the code. I like the idea to add the count of N as ambigous and plot on top of it. It is much clear to see the drop off. I will merge the code and review the code a bit more since the output plot seems not function correctly with all options. I also like to expose the min coverage as parameter to let user define the ambigous N and default to 10.

[lskatz]

Thank you! And once again thank you for this repo!