void print_help()
{
- fprintf(stdout,
+ fprintf(stdout,
"fastq-grep [OPTION]... PATTERN [FILE]...\n"
"Search for PATTERN in the read sequences in each FILE or standard input.\n"
"PATTERN, by default, is a perl compatible regular expression.\n\n"
"Options:\n"
+" -i, --id match the read id (by default, sequence is matched)\n"
" -v, --invert-match select nonmatching entries\n"
+" -m, --mismatches=FILE output mismatching entries to the given file\n"
" -c, --count output only the number of matching sequences\n"
" -h, --help print this message\n"
" -V, --version output version information and exit\n"
static int invert_flag;
static int count_flag;
+static int id_flag;
-void fastq_grep(FILE* fin, FILE* fout, pcre* re)
+void fastq_grep(FILE* fin, FILE* fout, FILE* mismatch_file, pcre* re)
{
int rc;
int ovector[3];
size_t count = 0;
- 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_read(fqf, seq)) {
- while (fastq_next(fqf, seq)) {
rc = pcre_exec(re, /* pattern */
- NULL, /* extre data */
- seq->seq.s, /* subject */
- seq->seq.n, /* subject length */
+ NULL, /* extra data */
+ id_flag ? seq->id1.s : seq->seq.s,
+ id_flag ? seq->id1.n : seq->seq.n,
0, /* subject offset */
0, /* options */
ovector, /* output vector */
3 ); /* output vector length */
- if ((invert_flag && rc == PCRE_ERROR_NOMATCH) || rc >= 0) {
+ if ((invert_flag && rc == PCRE_ERROR_NOMATCH) || (!invert_flag && rc >= 0)) {
if (count_flag) count++;
else fastq_print(fout, seq);
}
+ else if (mismatch_file) {
+ fastq_print(mismatch_file, seq);
+ }
}
- fastq_free_seq(seq);
- fastq_close(fqf);
+ seq_free(seq);
+ fastq_free(fqf);
if (count_flag) fprintf(fout, "%zu\n", count);
}
invert_flag = 0;
count_flag = 0;
+ id_flag = 0;
int opt;
int opt_idx;
+ FILE* mismatch_file = NULL;
static struct option long_options[] =
- {
+ {
+ {"id", no_argument, &id_flag, 1},
{"invert-match", no_argument, &invert_flag, 1},
+ {"mismatches", required_argument, NULL, 'm'},
{"count", no_argument, &count_flag, 1},
{"help", no_argument, NULL, 'h'},
{"version", no_argument, NULL, 'V'},
};
while (1) {
- opt = getopt_long(argc, argv, "vchV", long_options, &opt_idx);
+ opt = getopt_long(argc, argv, "ivmchV", long_options, &opt_idx);
- if( opt == -1 ) break;
+ if (opt == -1) break;
switch (opt) {
case 0:
}
break;
+ case 'i':
+ id_flag = 1;
+ break;
+
case 'v':
invert_flag = 1;
break;
+ case 'm':
+ mismatch_file = fopen(optarg, "w");
+ if (mismatch_file == NULL) {
+ fprintf(stderr, "No such file '%s'.\n", optarg);
+ return 1;
+ }
+ break;
+
case 'c':
count_flag = 1;
break;
if (optind >= argc || (argc - optind == 1 && strcmp(argv[optind],"-") == 0)) {
- fastq_grep(stdin, stdout, re);
+ fastq_grep(stdin, stdout, mismatch_file, re);
}
else {
for (; optind < argc; optind++) {
continue;
}
- fastq_grep(fin, stdout, re);
+ fastq_grep(fin, stdout, mismatch_file, re);
fclose(fin);
}
}
pcre_free(re);
+ if (mismatch_file) fclose(mismatch_file);
return 0;
}