BFCounter/fastq.cpp at master · pmelsted/BFCounter · GitHub

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#include <stdio.h>
#include <string.h>
#include <zlib.h>

#include "kseq.h"
#include "fastq.hpp"


FastqFile::FastqFile(const vector<string> files) : kseq(NULL), fnames(files) {
  fnit = fnames.begin();
  file_no = 0;
  fp = gzopen(fnit->c_str(), "r");
  kseq = kseq_init(fp);
}

FastqFile::~FastqFile() {
  close();
}

void FastqFile::reopen() {
  close();
  fnit = fnames.begin();
  fp = gzopen(fnit->c_str(), "r");
  kseq = kseq_init(fp);
}

// returns >=0 (length of seq), -1 end of last file, -2 truncated quality string
int FastqFile::read_next(char *read, size_t *read_len, char *seq, size_t *seq_len, unsigned int *file_id, char* qual) {
    int r;
    r = kseq_read(kseq);
    if (r>=0) {
      memcpy(read, kseq->name.s, kseq->name.l+1); // 0-terminated string
      *read_len = kseq->name.l;
      memcpy(seq, kseq->seq.s, kseq->seq.l+1); // 0-terminated string
      *seq_len = kseq->seq.l;
      if (qual != NULL) {
	memcpy(qual, kseq->qual.s, kseq->qual.l+1); // 0-terminated string
      }
      if (file_id != NULL) {
	*file_id = file_no/2;
      }
    } else if (r == -1) {
      open_next();
      if (fnit != fnames.end()) {
	return read_next(read,read_len,seq,seq_len,file_id);
      } else {
	return -1;
      }
    }
    return r;
  }

vector<string>::const_iterator FastqFile::open_next() {
  if (fnit != fnames.end()) {
    // close current file
    kseq_destroy(kseq);
    gzclose(fp);
    kseq = NULL;

    // get next file
    ++fnit;
    ++file_no;
    if (fnit != fnames.end()) {
      fp = gzopen(fnit->c_str(),"r");
      kseq = kseq_init(fp);
    }
  }
  return fnit;
}

void FastqFile::close() {
  if (kseq != NULL) {
    kseq_destroy(kseq);
    kseq = NULL;
    gzclose(fp);
    fnit = fnames.end();
  }
}