read from stdin if -i not supplied, also add strerror for information if opening file doesn't work:fgmutant-refactor-total-count

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);