diff options
| -rw-r--r-- | kmer_total_count.c | 41 |
1 files changed, 35 insertions, 6 deletions
diff --git a/kmer_total_count.c b/kmer_total_count.c index ec9a3f8..cc9e625 100644 --- a/kmer_total_count.c +++ b/kmer_total_count.c @@ -9,13 +9,16 @@ int main(int argc, char **argv) { unsigned long long i = 0; + long long j = 0; - if(argc != 3) { - fprintf(stderr, "Please supply a filename and a kmer\n"); + 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); } unsigned long kmer = atoi(argv[2]); + unsigned long long width = pow_four(kmer); + if(kmer == 0) { fprintf(stderr, "Error: invalid kmer.\n"); exit(EXIT_FAILURE); @@ -25,8 +28,34 @@ int main(int argc, char **argv) { // print out our counts arrray // manually unrolled 4 loops to reduce fprintf calls - for(i = 0; i < pow_four(atoi(argv[2])); i=i+4) - fprintf(stdout, "%llu\n%llu\n%llu\n%llu\n", counts[i], counts[i+1], counts[i+2], counts[i+3]); - - return EXIT_SUCCESS; + + if(argc == 3) { + 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; } |