Unclear details of max-cov.py #15
Description
I've been playing around with the test files a bit, and had a look at the max-cov.py script, and am a bit confused about the details.
First, when setting the cutoff to 0.5 instead of the 0.7 that is used in the test script, the results do not change. The pileup file for instance contains four positions on X, for the first sample with three 5X and one 9X read depth (coverage) positions. With a 0.5 threshold/cutoff, I'd expect the tool to report 5X as the max-depth, as 75% of the positions have that coverage. Instead, the script reports 9X. I've tried to see why this is happening, but could not quite get to the bottom of that yet.
Second, it seems that the script only considers positions that are actually present in the pileup file. In the test file, those are not consecutive, and we can hence assume that all missing positions have zero coverage. Shouldn't those also be taken into account? I am not sure, and hence would like to hear your thoughts on why or why not.
Cheers and so long
Lucas