pblischak / polyploid-genotyping Goto Github PK

Hi Paul,
I tried installing EBG on our machine running Ubuntu 18.04. When I ran make, I got the error "'isnan' was not declared in this scope", as well as suggestions to use std::isnan.
Lindsay

The log likelihoods of the different models are computed using log sums of exponentials, which can have nasty overflow/underflow problems (cf. this link). I've run into this problem when read counts are high (on the order of ~1000x). Since sequencing coverage isn't typically this high, it hopefully should be an issue for most data sets. Nevertheless, I'll need to fix it.

The way that I am storing the input data (total and alt reads) is to push them linearly into an integer vector. A user has noted that large data sets will not be read in properly due to a presumed memory error (I haven't verified this yet), so the program will not run. I am planning to try to fix it by making the input data two-dimensional vectors to see if that will fix the issue.

# Current implementation
std::vector<int> input;

# New implementation
# with 2D vector
std::vector< std::vector<int> > input;