diff options
| -rw-r--r-- | kmer_total_count.c | 121 |
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; |