This script is used to gather the error statistic.
verify takes the called snps as input and checks to make sure they are correct. If the snps at a location is "unknown", the verifier just tracks that it was unknown.
It was possible to get stuck in an infinite loop if the entire read was one value. Also, it didn't work at all, but now it does.
using --error (or -e) you can set the probability that a read will contain an error. An error in a read is simply a read having a wrong value for a position. The default for -e is 0, so that reads can be generated as they were genereated before.
We cannot simply look for differences and record them, we must make a record for each location so we know the coverage (number of reads) for that position.
Simple snp caller with a consensus based method. Actually right now it's just a max based method.
Generates SNPs by replacing a letter in a FASTA sequence. The probability of replacing the letter is given by the user.
Generates reads of any length with a specified amount of coverage from a reference FASTA sequence.
Generates sequences of DNA of any length.