fataltes

import pandas as pd
import numpy as np

class GCModel:
    def __init__(self):
        self.obs_weights_ = None
        self.exp_weights_ = None
        self.obs_ = None
        self.exp_ = None
        self.dims_ = None

fataltes

#!/usr/bin/env python
import sys, os
if len(sys.argv) < 4:
    print("alters BCALM's unitigs so that they fit pufferfish input. more specifically:")
    print("  the script considers the set B and E of all k-mers that are extremities of the reference genomes, respectively beginning and end of genomes.")
    print("  output is: modified unitigs such that each k-mer in B should be the beginning of an unitig, and each kmer in E should be end of an unitig.")
    print("  in order words, unitigs are split at kmers that are extremities of the reference sequences")
    exit("arguments: references.fa unitigs.fa k")

references=sys.argv[1]

fataltes

int main(int argc, char *argv[]) {


  uint16_t num_samples = 2586;
  std::string filename = argv[1];
  BitVectorRRR eqcls(filename);
  size_t totalEqClsCnt = eqcls.bit_size()/num_samples; //222584822;
  std::cout << "Total bit size: " << eqcls.bit_size() << "\ntotal # of equivalence classes: " << totalEqClsCnt << "\n";
  size_t gigs = 8;
  std::string dir = "bvs_8g";

fataltes

int getPufferfishContigStats(IndexT& pi) {
  //size_t k = pi.k();
  CanonicalKmer::k(pi.k());
  size_t found = 0;
  size_t notFound = 0;
  size_t correctPosCntr = 0;
  size_t incorrectPosCntr = 0;
  size_t numTrueTxp = 0;
  size_t numLostTxp = 0;
  std::ofstream out("contigInfo.txt");