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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"); |
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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"; |
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#!/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] |
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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 |