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Commits on May 29, 2009
  1. Add gatherStats script

    This script is used to gather the error statistic.
    committed May 29, 2009
Commits on May 28, 2009
Commits on May 24, 2009
  1. Add snp verifier

    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.
    committed May 23, 2009
Commits on May 23, 2009
  1. readGen: better error generation

    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.
    committed May 23, 2009
Commits on May 19, 2009
  1. readGen: introduce error option

    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.
    committed May 19, 2009
  2. caller: A correct, but naive consensus method

    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.
    committed May 19, 2009
Commits on May 18, 2009
  1. Add snp caller

    Simple snp caller with a consensus based method. Actually right now it's
    just a max based method.
    committed May 18, 2009
Commits on May 14, 2009
  1. Add SNP generator

    Generates SNPs by replacing a letter in a FASTA sequence. The
    probability of replacing the letter is given by the user.
    committed May 14, 2009
  2. Add read generator

    Generates reads of any length with a specified amount of coverage from a
    reference FASTA sequence.
    committed May 14, 2009
  3. Add sequence generator

    Generates sequences of DNA of any length.
    committed May 14, 2009
  4. Start project, setup .gitignore

    committed May 14, 2009