*/
-#include "fastq-common.h"
-#include "fastq-parse.h"
+#include "common.h"
+#include "parse.h"
#include <stdio.h>
#include <string.h>
#include <getopt.h>
#endif
+static const char* prog_name = "fastq-grep";
+
+
void print_help()
{
- fprintf( stderr,
+ 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"
-" -h, --help print this message\n"
+" -i, --id match the read id (by default, sequence is matched)\n"
" -v, --invert-match select nonmatching entries\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 help_flag;
static int count_flag;
+static int id_flag;
-void print_fastq_entry(FILE* fout, seq_t* seq)
-{
- fprintf(fout, "@%s\n%s\n+%s\n%s\n",
- seq->id1.s,
- seq->seq.s,
- seq->id2.s,
- seq->qual.s );
-}
-
-
void fastq_grep(FILE* fin, FILE* fout, pcre* re)
{
int rc;
seq_t* seq = fastq_alloc_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 print_fastq_entry(fout, seq);
+ else fastq_print(fout, seq);
}
}
invert_flag = 0;
- help_flag = 0;
count_flag = 0;
+ id_flag = 0;
int opt;
int opt_idx;
static struct option long_options[] =
{
- {"help", no_argument, &help_flag, 1},
+ {"id", no_argument, &id_flag, 1},
{"invert-match", no_argument, &invert_flag, 1},
- {"count", no_argument, &count_flag, 1},
+ {"count", no_argument, &count_flag, 1},
+ {"help", no_argument, NULL, 'h'},
+ {"version", no_argument, NULL, 'V'},
{0, 0, 0, 0}
};
while (1) {
- opt = getopt_long(argc, argv, "hvc", long_options, &opt_idx);
+ opt = getopt_long(argc, argv, "ivchV", long_options, &opt_idx);
- if( opt == -1 ) break;
+ if (opt == -1) break;
switch (opt) {
case 0:
}
break;
- case 'h':
- help_flag = 1;
+ case 'i':
+ id_flag = 1;
break;
case 'v':
count_flag = 1;
break;
+ case 'h':
+ print_help();
+ return 0;
+
+ case 'V':
+ print_version(stdout, prog_name);
+ return 0;
+
case '?':
return 1;
}
}
- if (help_flag) {
- print_help();
- return 0;
- }
-
if (optind >= argc) {
fprintf(stderr, "A pattern must be specified.\n");
return 1;