void print_help()
{
fprintf(stdout,
-"fastq-sample [OPTION]... [FILE [FILE2]]\n"
+"fastq-sample [OPTION]... FILE [FILE2]\n"
"Sample random reads from a FASTQ file."
"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"
+" -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"
+" they are not output).\n"
" -r, --with-replacement sample with relpacement\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(const char* prefix, FILE* file1, FILE* file2, unsigned long k, double p)
+void fastq_sample(unsigned long rng_seed,
+ const char* prefix, const char* cprefix,
+ FILE* file1, FILE* file2, unsigned long k, double p)
{
/*
* The basic idea is this:
}
rng_t* rng = fastq_rng_alloc();
+ fastq_rng_seed(rng, rng_seed);
unsigned long* xs;
if (replacement_flag) xs = index_with_replacement(rng, n, k);
}
+ /* open complement output */
+ FILE* cfout1 = NULL;
+ FILE* cfout2 = NULL;
+
+ if (cprefix != NULL && file2 == NULL) {
+ output_len = strlen(cprefix) + 7;
+ output_name = malloc_or_die((output_len + 1) * sizeof(char));
+
+ snprintf(output_name, output_len, "%s.fastq", cprefix);
+ cfout1 = fopen(output_name, "wb");
+ if (cfout1 == NULL) {
+ fprintf(stderr, "Cannot open file %s for writing.\n", output_name);
+ exit(1);
+ }
+
+ cfout2 = NULL;
+
+ free(output_name);
+ }
+ else if (cprefix != NULL) {
+ output_len = strlen(cprefix) + 9;
+ output_name = malloc_or_die((output_len + 1) * sizeof(char));
+
+ snprintf(output_name, output_len, "%s.1.fastq", cprefix);
+ cfout1 = fopen(output_name, "wb");
+ if (cfout1 == NULL) {
+ fprintf(stderr, "Cannot open file %s for writing.\n", output_name);
+ exit(1);
+ }
+
+ snprintf(output_name, output_len, "%s.2.fastq", cprefix);
+ cfout2 = fopen(output_name, "wb");
+ if (cfout1 == NULL) {
+ fprintf(stderr, "Cannot open file %s for writing.\n", output_name);
+ exit(1);
+ }
+
+ free(output_name);
+ }
+
+
unsigned long i = 0; // read number
unsigned long j = 0; // index into xs
}
}
- while (j < k && xs[j] == i) {
- fastq_print(fout1, seq1);
- if (f2 != NULL) fastq_print(fout2, seq2);
- ++j;
+ if (xs[j] == i) {
+ while (j < k && xs[j] == i) {
+ fastq_print(fout1, seq1);
+ if (f2 != NULL) fastq_print(fout2, seq2);
+ ++j;
+ }
+ }
+ else if (cfout1 != NULL) {
+ fastq_print(cfout1, seq1);
+ if (f2 != NULL) fastq_print(cfout2, seq2);
}
++i;
fclose(fout1);
if (fout2 != NULL) fclose(fout2);
+ if (cfout1 != NULL) fclose(cfout1);
+ if (cfout2 != NULL) fclose(cfout2);
+
fastq_rng_free(rng);
free(xs);
}
int opt_idx;
const char* prefix = NULL;
+ 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'},
- {"output", no_argument, NULL, 'o'},
- {"help", no_argument, NULL, 'h'},
- {"version", no_argument, NULL, 'V'},
+ {"with-replacement", no_argument, NULL, 'r'},
+ {"complement-output", required_argument, NULL, 'c'},
+ {"seed", required_argument, NULL, 's'},
+ {"output", no_argument, NULL, 'o'},
+ {"help", no_argument, NULL, 'h'},
+ {"version", no_argument, NULL, 'V'},
{0, 0, 0, 0}
};
replacement_flag = 0;
while (1) {
- opt = getopt_long(argc, argv, "n:p:o:rhV", long_options, &opt_idx);
+ opt = getopt_long(argc, argv, "n:p:o:rs:hV", long_options, &opt_idx);
if( opt == -1 ) break;
replacement_flag = 1;
break;
+ case 's':
+ rng_seed = strtoul(optarg, NULL, 10);
+ break;
+
case 'o':
prefix = optarg;
break;
+ case 'c':
+ cprefix = optarg;
+ break;
+
case 'h':
print_help();
return 0;
char* prefix_alloc = NULL;
if (optind >= argc) {
- file1 = stdin;
+ fputs("An input file must be given.\n", stderr);
+ print_help();
+ exit(1);
}
else {
- if (strcmp(argv[optind], "-") == 0) {
- file1 = stdin;
- if (prefix == NULL) prefix = "stdin.sample";
+ file1 = fopen(argv[optind], "rb");
+ if (file1 == NULL) {
+ fprintf(stderr, "Cannot open '%s' for reading.\n", argv[optind]);
+ return 1;
}
- 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;
- }
+ 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;
if (optind < argc) {
- if (strcmp(argv[optind], "-") == 0) {
- if (file1 == stdin) {
- fprintf(stderr, "Both input files cannot be standard input.\n");
- return 1;
- }
- file2 = stdin;
- }
- else {
- file2 = fopen(argv[optind], "rb");
- if (file2 == NULL) {
- fprintf(stderr, "Cannot open '%s' for reading.\n", argv[optind]);
- return 1;
- }
+ file2 = fopen(argv[optind], "rb");
+ if (file2 == NULL) {
+ fprintf(stderr, "Cannot open '%s' for reading.\n", argv[optind]);
+ return 1;
}
}
}
- fastq_sample(prefix, file1, file2, k, p);
+ fastq_sample(rng_seed, prefix, cprefix, file1, file2, k, p);
free(prefix_alloc);
return 0;