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fqcounter.cpp
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fqcounter.cpp
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#include <zlib.h>
#include <stdio.h>
#include "kseq.h"
#include <omp.h>
#include <getopt.h>
#include <libgen.h>
#include <iostream>
#include <iomanip>
#include <map>
// reference: http://lh3lh3.users.sourceforge.net/parsefastq.shtml
// reference: https://github.com/billzt/readfq
// Andrew Warry ADAC 15-02-2016
//
KSEQ_INIT(gzFile, gzread)
int main(int argc, char *argv[])
{
// gzFile fp;
// kseq_t *seq;
// int l;
int threadnum;
int c;
int bflag = 0;
int hflag = 0;
int lflag = 0;
int oflag = 0;
int tvalue = 0;
int nprocs = sysconf(_SC_NPROCESSORS_CONF);
while( ( c = getopt (argc, argv, "t:bhol") ) != -1 )
{
switch(c)
{
case 'b':
bflag =1;
break;
case 'l':
lflag =1;
break;
case 'h':
hflag =1;
break;
case 'o':
oflag =1;
break;
case 't':
if(optarg) tvalue = atoi(optarg) ;
break;
}
}
// printf("nprocs: %d\n", nprocs);
if(lflag ==1){
bflag =1;
}
if(tvalue){
threadnum = tvalue;
}else{
threadnum = 2;
}
// printf("threads: %d\n", threadnum);
if(threadnum >= nprocs){
threadnum = (nprocs -1);
fprintf(stderr, "## threads to use reset to: %d\n", threadnum);
}
// printf("threads: %d\n", threadnum);
if ((argc == 1)||(hflag == 1)){
fprintf(stderr, "%s is a tool to count reads in fastq/fastq.gz/fasta/fasta.gz files\n\n", basename(argv[0]));
fprintf(stderr, "Usage: %s <*fastq>\n", basename(argv[0]));
fprintf(stderr, " %s -b -t <int> <*fastq.gz>\n", basename(argv[0]));
fprintf(stderr, "\n\t-b Add a basecount column\n");
fprintf(stderr, "\n\t-l Add basecount and mean length columns\n");
fprintf(stderr, "\n\t-t <int> [2] Select number of threads\n");
fprintf(stderr, "\t Note: one fastq file/thread\n");
fprintf(stderr, "\n\t-o Delayed ordered output\n");
fprintf(stderr, "\n\t-h This message\n\n");
return 1;
}
// int i;
//#pragma omp parallel
//std::map<std::string, long> count_results;
// if(bflag == 1){
std::map<std::string, std::pair<long, long> > count_results2;
// } else {
std::map<std::string, long> count_results;
// }
#pragma omp parallel for num_threads(threadnum)
for(int i = optind; i < argc; ++i ) {
// for(int i = 1; i < argc; ++i ) {
// printf( "argv[ %d ] = %s\n", i, argv[i] );
// }
gzFile fp;
kseq_t *seq;
int l;
long int n = 0, slen = 0;
fp = gzopen(argv[i], "r"); // open the file handler
seq = kseq_init(fp); // initialize seq
if(bflag == 1){
while ((l = kseq_read(seq)) >= 0) { // STEP 4: read sequence
++n, slen += seq->seq.l;
}
// printf("%s\tread_count:%ld\tbase_count:%ld\n", argv[i], n, slen);
if(oflag){
count_results2[argv[i]] = std::make_pair(n, slen );
} else {
if(lflag){
float avgl = slen / n;
printf("%s\t%ld\t%ld\t%.0f\n", argv[i], n, slen, avgl);
} else {
printf("%s\t%ld\t%ld\n", argv[i], n, slen);
}
}
// printf("%s\t%ld\n", argv[i], n);
}else{
while ((l = kseq_read(seq)) >= 0) { // STEP 4: read sequence
++n;//, slen += seq->seq.l;
}
// printf("%s\tread_count:%ld\tbase_count:%ld\n", argv[i], n, slen);
// printf("%s\t%ld\t%ld\n", argv[i], n, slen);
if(oflag == 1){
count_results[argv[i]] = n ;
} else {
printf("%s\t%ld\n", argv[i], n);
}
}
kseq_destroy(seq); // STEP 5: destroy seq
gzclose(fp); // STEP 6: close the file handler
}
//std::cout << "================\n";
if((oflag == 1)&&(bflag == 0)){
for(std::map<std::string, long>::const_iterator it = count_results.begin();
it != count_results.end(); ++it)
{
std::cout << it->first << "\t" << it->second << "\n";
}
}
std::cout << std::setprecision(0) << std::fixed;
// float avgl;
if((oflag == 1)&&(bflag == 1)){
for(std::map<std::string, std::pair<long, long> >::const_iterator it = count_results2.begin();
it != count_results2.end(); ++it)
{
// avgl = second.second/second.first;of
if(lflag == 1){
std::cout << it->first << "\t" << it->second.first << "\t" << it->second.second << "\t" << (it->second.second / it->second.first) << std::endl;
} else {
std::cout << it->first << "\t" << it->second.first << "\t" << it->second.second << std::endl;
}
}
}
return 0;
}