diff options
| -rw-r--r-- | kmer_total_count.c | 26 |
1 files changed, 20 insertions, 6 deletions
diff --git a/kmer_total_count.c b/kmer_total_count.c index 2de7036..0148eae 100644 --- a/kmer_total_count.c +++ b/kmer_total_count.c @@ -27,9 +27,12 @@ void help() { "dna-utils. Drexel University, Philadelphia USA, 2014;\n" "software available at www.github.com/EESI/dna-utils/\n"); } + + int main(int argc, char **argv) { - char *filename = NULL; + char *fn = NULL; + FILE *fh = NULL; unsigned int kmer = 0; @@ -62,7 +65,7 @@ int main(int argc, char **argv) { switch (c) { case 'i': - filename = optarg; + fn = optarg; break; case 'k': kmer = atoi(optarg); @@ -81,11 +84,22 @@ int main(int argc, char **argv) { break; } } - if(filename == NULL) { - fprintf(stderr, "Error: filename (-i) must be supplied\n"); + if(argc == 1) { + help(); exit(EXIT_FAILURE); } - if(kmer == 0 && !kmer_set) { + if(fn == NULL) { + fprintf(stderr, "no input file specified with -i, reading from stdin\n"); + fh = stdin; + } + else { + fh = fopen(fn, "r"); + if(fh == NULL) { + fprintf(stderr, "Could not open %s - %s\n", fn, strerror(errno)); + exit(EXIT_FAILURE); + } + } + if(!kmer_set) { fprintf(stderr, "Error: kmer (-k) must be supplied\n"); exit(EXIT_FAILURE); } @@ -96,7 +110,7 @@ int main(int argc, char **argv) { width = pow_four(kmer); - unsigned long long *counts = get_kmer_counts_from_file(filename, kmer); + unsigned long long *counts = get_kmer_counts_from_file(fh, kmer); // If nonzero is set, only print non zeros if(nonzero) { |