Potential memory error

[pblischak]

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;