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-rw-r--r--kmer_total_count.c17
1 files changed, 9 insertions, 8 deletions
diff --git a/kmer_total_count.c b/kmer_total_count.c
index 2f944d8..2b4f548 100644
--- a/kmer_total_count.c
+++ b/kmer_total_count.c
@@ -62,9 +62,16 @@ int main(int argc, char **argv) {
}
}
if(filename == NULL) {
- fprintf(stderr, "Error: filename (-i) must be supplied\n");
- exit(EXIT_FAILURE);
+ fprintf(stderr, "not input file specified with -i, reading from stdin\n");
+ fh = stdin;
}
+ else {
+ fh = fopen(filename, "r");
+ if(fh == NULL) {
+ fprintf(stderr, "Could not open %s - %s\n", filename, strerror(errno));
+ exit(EXIT_FAILURE);
+ }
+ }
if(kmer == 0 && !kmer_set) {
fprintf(stderr, "Error: kmer (-k) must be supplied\n");
exit(EXIT_FAILURE);
@@ -74,12 +81,6 @@ int main(int argc, char **argv) {
exit(EXIT_FAILURE);
}
- fh = fopen(filename, "r");
- if(fh == NULL) {
- fprintf(stderr, "Could not open %s\n", filename);
- exit(EXIT_FAILURE);
- }
-
width = kmer_pow_four(kmer);
unsigned long long *counts = kmer_counts_from_file(fh, kmer);