allow for kmer inference and fix memory leak in get_fasta_files_from_file

1 files changed, 5 insertions, 7 deletions

diff --git a/src/c/quikr.c b/src/c/quikr.c
index de1f39a..5ed72b0 100644
--- a/src/c/quikr.c
+++ b/src/c/quikr.c
@@ -131,25 +131,23 @@ int main(int argc, char **argv) {
 		exit(EXIT_FAILURE);
 	}
 
+	// load sensing matrix
+	struct matrix *sensing_matrix = load_sensing_matrix(sensing_matrix_filename, kmer);
+
 	if(kmer == 0) {
-		fprintf(stderr, "Error: zero is not a valid kmer\n");
-		exit(EXIT_FAILURE);
+		fprintf(stdout, "Warning: zero is not a valid kmer, inferring kmer from sensing matrix\n");
+		kmer = sensing_matrix->kmer;
 	}
 
-
 	// 4 "ACGT" ^ Kmer gives us the size of output rows
 	width = pow_four(kmer);
 
-	// load sensing matrix
-	struct matrix *sensing_matrix = load_sensing_matrix(sensing_matrix_filename, kmer);
-
 	if(verbose) {
 		printf("width: %llu\n", width);
 		printf("sequences: %llu\n", sensing_matrix->sequences);
 	}
 
 
-
 	// load counts matrix
 	double *count_matrix = malloc(width * sizeof(double));
 	check_malloc(count_matrix, NULL);