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-rw-r--r--kmer_total_count.c121
1 files changed, 87 insertions, 34 deletions
diff --git a/kmer_total_count.c b/kmer_total_count.c
index fd8a676..b0bf23f 100644
--- a/kmer_total_count.c
+++ b/kmer_total_count.c
@@ -1,59 +1,112 @@
// Copyright 2013 Calvin Morrison
#include <errno.h>
+#include <stdbool.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
+#include <getopt.h>
#include "kmer_utils.h"
int main(int argc, char **argv) {
+
+ char *filename = NULL;
+
+ unsigned int kmer = NULL;
+
+ bool nonzero = 0;
+ bool label = 0;
+ bool kmer_set = 0;
+
+ unsigned long long width = 0;
+
unsigned long long i = 0;
+
long long j = 0;
- if(argc < 3) {
- fprintf(stderr, "Please supply a filename and a kmer, then as many kmers as you want (in ACGT format)\n");
- exit(EXIT_FAILURE);
- }
+ static struct option long_options[] = {
+ {"input", required_argument, 0, 'i'},
+ {"kmer", required_argument, 0, 'k'},
+ {"nonzero", no_argument, 0, 'n'},
+ {"label", no_argument, 0, 'l'},
+ {"help", no_argument, 0, 'h'},
+ {0, 0, 0, 0}
+ };
- unsigned long kmer = atoi(argv[2]);
- unsigned long long width = pow_four(kmer);
+ while (1) {
+ int option_index = 0;
+ int c = 0;
+
+ c = getopt_long (argc, argv, "i:k:nlvh", long_options, &option_index);
+
+ if (c == -1)
+ break;
+
+ switch (c) {
+ case 'i':
+ filename = optarg;
+ break;
+ case 'k':
+ kmer = atoi(optarg);
+ kmer_set = true;
+ break;
+ case 'n':
+ nonzero = true;
+ break;
+ case 'l':
+ label = true;
+ break;
+ case 'h':
+ printf("help-text\n");
+ exit(EXIT_SUCCESS);
+ default:
+ break;
+ }
+ }
+ if(filename == NULL) {
+ fprintf(stderr, "Error: filename (-i) must be supplied\n");
+ exit(EXIT_FAILURE);
+ }
+ if(kmer == NULL && !kmer_set) {
+ fprintf(stderr, "Error: kmer (-k) must be supplied\n");
+ exit(EXIT_FAILURE);
+ }
if(kmer == 0) {
- fprintf(stderr, "Error: invalid kmer.\n");
+ fprintf(stderr, "Error: invalid kmer - '%d'.\n", kmer);
exit(EXIT_FAILURE);
}
- unsigned long long *counts = get_kmer_counts_from_file(argv[1], atoi(argv[2]));
+ width = pow_four(kmer);
+
+ unsigned long long *counts = get_kmer_counts_from_file(filename, kmer);
- // print out our counts arrray
- // manually unrolled 4 loops to reduce fprintf calls
- if(argc == 3) {
+ // If nonzero is set, only print non zeros
+ if(nonzero) {
+ // if labels is set, print out our labels
+ if(label) {
+ for(i = 0; i < width; i++)
+ if(counts[i] != 0)
+ fprintf(stdout, "%s\t%llu\n", index_to_kmer(i, kmer),i, counts[i]);
+
+ }
+ else {
+ for(i = 0; i < width; i++)
+ if(counts[i] != 0)
+ fprintf(stdout, "%llu\t%llu\n", i, counts[i]);
+
+ }
+ }
+ // If we aren't printing nonzeros print everything
+ else {
+ if(label) {
+ for(i = 0; i < width; i++)
+ fprintf(stdout, "%s\t%llu\n", index_to_kmer(i, kmer), counts[i]);
+ }
+ else {
for(i = 0; i < width; i=i+4)
fprintf(stdout, "%llu\n%llu\n%llu\n%llu\n", counts[i], counts[i+1], counts[i+2], counts[i+3]);
- }
- else {
- for(i = 3; i < argc; i++) {
- unsigned long k = width;
- size_t len = 0;
- fprintf(stdout, "%s\t", argv[i]);
-
- len = strlen(argv[i]);
- if(len != kmer) {
- fprintf(stdout, "ERR\n");
- continue;
- }
- for(j = 0; j < len; j++)
- argv[i][j] = alpha[argv[i][j]];
-
- k = num_to_index(argv[i], kmer, width);
-
- if(k == width) {
- fprintf(stdout, "ERR\n");
- }
- else {
- fprintf(stdout, "%llu\n", counts[k]);
- }
}
}
return EXIT_SUCCESS;