* Sample reads with or without replacement from a FASTQ file.
*
*/
+#include <getopt.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "common.h"
#include "parse.h"
#include "rng.h"
-#include <stdlib.h>
-#include <stdio.h>
-#include <string.h>
-#include <getopt.h>
-#include <zlib.h>
-#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
-# include <fcntl.h>
-# include <io.h>
-# define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
-#else
-# define SET_BINARY_MODE(file)
-#endif
static const char* prog_name = "fastq-sample";
"Options:\n"
" -n N the number of reads to sample (default: 10000)\n"
" -p N the proportion of the total reads to sample\n"
-" -o, --output=PREFIX output file prefix\n"
+" -o, --output=PREFIX output file prefix\n (Default: \"sample\")"
" -c, --complement-output=PREFIX\n"
" output reads not included in the random sample to\n"
" a file (or files) with the given prefix (by default,\n"
" -s, --seed=SEED a manual seed to the random number generator\n"
" -h, --help print this message\n"
" -V, --version output version information and exit\n"
- );
+);
}
void fastq_sample(unsigned long rng_seed,
- const char* prefix, const char* cprefix,
- FILE* file1, FILE* file2, unsigned long k, double p)
+ const char* prefix, const char* cprefix,
+ FILE* file1, FILE* file2, unsigned long k, double p)
{
- /*
- * The basic idea is this:
- *
- * 1. Count the number of lines in the file, n.
- *
- * 2a. If sampling with replacement, generate k random integers in [0, n-1].
- *
- * 2b. If sampling without replacement, generate a list of integers 0..(n-1),
- * shuffle with fisher-yates, then consider the first k.
- *
- * 3. Sort the integer list.
- *
- * 3. Read through the file again, when the number at the front of the integer
- * list matches the index of the fastq etry, print the entry, and pop the
- * number.
- */
+ /*
+ * The basic idea is this:
+ *
+ * 1. Count the number of lines in the file, n.
+ *
+ * 2a. If sampling with replacement, generate k random integers in [0, n-1].
+ *
+ * 2b. If sampling without replacement, generate a list of integers 0..(n-1),
+ * shuffle with fisher-yates, then consider the first k.
+ *
+ * 3. Sort the integer list.
+ *
+ * 3. Read through the file again, when the number at the front of the integer
+ * list matches the index of the fastq etry, print the entry, and pop the
+ * number.
+ */
unsigned long n, n2;
if (f2 != NULL) fastq_rewind(f2);
if (p > 0.0) {
- k = (unsigned long) (p * (double) n);
+ k = (unsigned long) round(p * (double) n);
if (!replacement_flag && k > n) k = n;
}
qsort(xs, k, sizeof(unsigned long), cmpul);
-
/* open output */
FILE* fout1;
FILE* fout2;
output_name = malloc_or_die((output_len + 1) * sizeof(char));
snprintf(output_name, output_len, "%s.fastq", prefix);
- fout1 = fopen(output_name, "wb");
+ fout1 = open_without_clobber(output_name);
if (fout1 == NULL) {
fprintf(stderr, "Cannot open file %s for writing.\n", output_name);
exit(1);
output_name = malloc_or_die((output_len + 1) * sizeof(char));
snprintf(output_name, output_len, "%s.1.fastq", prefix);
- fout1 = fopen(output_name, "wb");
+ fout1 = open_without_clobber(output_name);
if (fout1 == NULL) {
fprintf(stderr, "Cannot open file %s for writing.\n", output_name);
exit(1);
}
snprintf(output_name, output_len, "%s.2.fastq", prefix);
- fout2 = fopen(output_name, "wb");
+ fout1 = open_without_clobber(output_name);
if (fout1 == NULL) {
fprintf(stderr, "Cannot open file %s for writing.\n", output_name);
exit(1);
free(output_name);
}
-
/* open complement output */
FILE* cfout1 = NULL;
FILE* cfout2 = NULL;
free(output_name);
}
-
-
unsigned long i = 0; // read number
unsigned long j = 0; // index into xs
int main(int argc, char* argv[])
{
- SET_BINARY_MODE(stdin);
- SET_BINARY_MODE(stdout);
-
int opt;
int opt_idx;
- const char* prefix = NULL;
- const char* cprefix = NULL;
+ const char* prefix = "sample";
+ const char* cprefix = NULL;
unsigned long rng_seed = 4357;
unsigned long k = 10000; // number of reads to sample
double p = -1; // proportion of reads to sample
-
static struct option long_options[] =
- {
+ {
{"with-replacement", no_argument, NULL, 'r'},
{"complement-output", required_argument, NULL, 'c'},
{"seed", required_argument, NULL, 's'},
FILE* file1 = NULL;
FILE* file2 = NULL;
- char* prefix_alloc = NULL;
-
if (optind >= argc) {
fputs("An input file must be given.\n", stderr);
print_help();
- exit(1);
+ return EXIT_FAILURE;
}
- else {
- file1 = fopen(argv[optind], "rb");
- if (file1 == NULL) {
- fprintf(stderr, "Cannot open '%s' for reading.\n", argv[optind]);
- return 1;
- }
- if (prefix == NULL) {
- /* guess at a reasonable output refix by trimming the
- * trailing file extension, if any. */
- char* tmp;
-
- /* base name */
- tmp = strrchr(argv[optind], '/');
- if (tmp != NULL) argv[optind] = tmp + 1;
-
- /* exclude file suffixes */
- tmp = strchr(argv[optind], '.');
- if (tmp == NULL) prefix = argv[optind];
- else {
- prefix_alloc = malloc_or_die((tmp - argv[optind] + 1) * sizeof(char));
- memcpy(prefix_alloc, argv[optind], (tmp - argv[optind]) * sizeof(char));
- prefix_alloc[tmp - argv[optind]] = '\0';
- prefix = prefix_alloc;
- }
- }
- ++optind;
+ file1 = fopen(argv[optind], "rb");
+ if (file1 == NULL) {
+ fprintf(stderr, "Cannot open '%s' for reading.\n", argv[optind]);
+ return 1;
+ }
- if (optind < argc) {
- file2 = fopen(argv[optind], "rb");
- if (file2 == NULL) {
- fprintf(stderr, "Cannot open '%s' for reading.\n", argv[optind]);
- return 1;
- }
+ if (++optind < argc) {
+ file2 = fopen(argv[optind], "rb");
+ if (file2 == NULL) {
+ fprintf(stderr, "Cannot open '%s' for reading.\n", argv[optind]);
+ return 1;
}
}
fastq_sample(rng_seed, prefix, cprefix, file1, file2, k, p);
- free(prefix_alloc);
- return 0;
+ return EXIT_SUCCESS;
}
-
-
-
-
-
-
-
projects / fastq-tools.git / blobdiff