}
-void fastq_match(FILE* fin, FILE* fout,
- sw_t* sw,
- unsigned char* query, int n)
+void fastq_match(FILE* fin, FILE* fout, sw_t* sw)
{
int score;
- fastq_t* fqf = fastq_open(fin);
- seq_t* seq = fastq_alloc_seq();
+ fastq_t* fqf = fastq_create(fin);
+ seq_t* seq = seq_create();
- while (fastq_next(fqf, seq)) {
+ while (fastq_read(fqf, seq)) {
fprintf(fout, "%s\t", seq->seq.s);
fastq_sw_conv_seq((unsigned char*)seq->seq.s, seq->seq.n);
fprintf(fout, "%d\n", score);
}
- fastq_free_seq(seq);
- fastq_close(fqf);
+ seq_free(seq);
+ fastq_free(fqf);
}
sw = fastq_alloc_sw(query, query_len);
if (optind >= argc || (argc - optind == 1 && strcmp(argv[optind],"-") == 0)) {
- fastq_match(stdin, stdout, sw, query, query_len);
+ fastq_match(stdin, stdout, sw);
}
else {
for (; optind < argc; optind++) {
continue;
}
- fastq_match(fin, stdout, sw, query, query_len);
+ fastq_match(fin, stdout, sw);
}
}