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looper_fastq.cpp
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looper_fastq.cpp
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/*
* Repeat identification in fastq files
* @file: hamSTR_fastq.cpp
* @author: Akshay Avvaru
* @version: 0.1 05/11/2020
*/
#include <fstream>
#include <iostream>
#include <math.h>
#include <string.h>
#include <unordered_map>
#include <vector>
#include "utils.h"
#include "fastq_reader.h"
using namespace std;
unordered_map<string, string> rclass_map;
unordered_map<string, uint> repeats_count;
unordered_map<string, unordered_map<uint, uint>> repeats_length_freq;
/*
* Update repeats
* @param repeat_class Repeat class
* @param rlen Length of the repeat
* @param repeats_count Reference for the unordered_map tracking repeats count
* @param repeats_length_freq Reference for the unordered_map tracking length wise frequency
*/
void update_result( string repeat_class, uint rlen,
unordered_map<string, uint> &repeats_count,
unordered_map<string, unordered_map<uint, uint>> &repeats_length_freq )
{
if (repeats_count.find(repeat_class) != repeats_count.end()) {
repeats_count[repeat_class] += 1;
if (repeats_length_freq[repeat_class].find(rlen) != repeats_length_freq[repeat_class].end()) {
repeats_length_freq[repeat_class][rlen] += 1;
}
else {
repeats_length_freq[repeat_class][rlen] = 1;
}
}
else {
repeats_count[repeat_class] = 1;
repeats_length_freq[repeat_class][rlen] = 1;
}
}
int main(int argc, char *argv[]) {
ios_base::sync_with_stdio(false);
string fin, fout;
uint m = 0, M = 0, cutoff = 0, d = 0;
if (argc == 1) { utils::print_help(); exit (EXIT_FAILURE); }
else if (argc > 1) {
utils::parse_arguments(argc, argv, fin, fout, m, M, cutoff);
utils::length_cutoff_error(M, cutoff);
}
fastq::FastqFile ins; ins.parse(fin);
utils::input_file_error(ins.ins.good(), fin);
ofstream out(fout);
ofstream filterOut(fin + "_looper.filtered.fastq");
utils::bitSeqWindow window;
cout << endl << "Searching for tandem repeats in " << fin << endl;
cout << "Min-motif: " << m << "\t Max-motif: " << M;
cout << "\t Length-cutoff: " << cutoff << endl;
uint64_t start_time = duration_cast<milliseconds>(
system_clock::now().time_since_epoch()
).count();
// integer tracking the start of the repeat
// -1 indicates no repeat is found
int start = -1;
uint atomicity, end, rlen;
string motif, repeat_class, orientation, seq_name;
int window_repeat_check = 0; // current window repeat check
// bitstring to retrieve window sequence with AND operation
const uint64_t NORM = ~(0ull) >> 2*(32-cutoff);
// non-redundant list of motifs used for checks
vector<uint> motif_checks = utils::get_motif_sizes(m, M);
const uint N = motif_checks.size();
uint extract_first[N];
uint64_t extract_second[N];
for (uint i = 0; i < N; i++) {
extract_first[i] = 2 * motif_checks[i]; // shift twice of motif size
extract_second[i] = NORM >> ( 2 * ( cutoff - motif_checks[i] ));
}
fastq::Read curr_read = ins.fetch();
while(curr_read.valid) {
window.reset();
bool filter = false;
for(const auto c: curr_read.sequence) {
switch(c) {
case 'a': case 'A': break;
case 'c': case 'C': window.seq |= 1ull; break;
case 'g': case 'G': window.seq |= 2ull; break;
case 't': case 'T': window.seq |= 3ull; break;
case 'N': case 'n':
// resets the window when an N is encountered
window.seq = 0; window.cutoff = -1;
if (start != -1) {
filter = true;
end = window.count - 1; rlen = end - start;
update_result(repeat_class, rlen, repeats_count, repeats_length_freq);
}
start = -1;
break;
default: continue;
}
window.count += 1;
window.cutoff += 1;
window.seq &= NORM;
if (window.cutoff >= cutoff) {
window_repeat_check = 0;
for (int i=0; i<N; ++i){
for (int i=0; i<N; ++i){
if ( (window.seq % divisor[i]) == ( window.seq >> rem_shift[i]) ) {
if (start == -1) {
filter = true;
start = window.count - cutoff;
atomicity = utils::check_atomicity(window.seq, cutoff, motif_checks[i]);
motif = utils::bit2base(window.seq, cutoff, atomicity);
if (rclass_map.find(motif) != rclass_map.end()) {
repeat_class = rclass_map[motif];
orientation = repeat_class.substr(atomicity, 1);
repeat_class = repeat_class.substr(0, atomicity);
}
else {
repeat_class = utils::get_repeat_class(window.seq, cutoff, atomicity, rclass_map);
orientation = repeat_class.substr(atomicity, 1);
repeat_class = repeat_class.substr(0, atomicity);
}
}
window_repeat_check = 1; break;
}
}
}
if (window_repeat_check == 0 & start != -1) {
filter = true;
end = window.count - 1; rlen = end - start;
update_result(repeat_class, rlen, repeats_count, repeats_length_freq);
start = -1;
}
}
window.seq <<= 2;
}
// if reat ends in a repeat
if (start != -1) {
filter = true;
end = window.count - 1; rlen = end - start;
update_result(repeat_class, rlen, repeats_count, repeats_length_freq);
start = -1;
}
// if repeat is found put read in filtered fastq file
if (filter) {
filterOut << curr_read.identifier << "\n";
filterOut << curr_read.sequence << "\n";
filterOut << curr_read.separator << "\n";
filterOut << curr_read.baseQual << "\n";
}
curr_read = ins.fetch();
}
out << "#Total reads: " << ins.currentCount() << "\n";
for (auto it = repeats_count.begin(); it != repeats_count.end(); it++) {
uint reads = ins.currentCount();
out << it->first << "\t" << it->second << "\t" << (float(it->second)/float(reads))*100000 << "\t";
for (auto jt = repeats_length_freq[it->first].begin(); jt != repeats_length_freq[it->first].end(); jt++) {
out << jt->first << "-" << jt->second << ";";
}
out << "\n";
}
out.close();
filterOut.close();
return EXIT_SUCCESS;
}