From dd39482f495a660d125ed9b4a352993a47e9d7d9 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Mon, 24 Feb 2014 12:17:15 -0500
Subject: add more verbose error messages and add more memory checks

---
 kmer_counts_per_sequence.c | 18 +++++++++++-------
 kmer_utils.c               |  8 +++++---
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/kmer_counts_per_sequence.c b/kmer_counts_per_sequence.c
index 2b95ed1..bd18f04 100644
--- a/kmer_counts_per_sequence.c
+++ b/kmer_counts_per_sequence.c
@@ -131,8 +131,10 @@ int main(int argc, char **argv) {
 	if(specific_mers) {
 		sparse = false;
 		desired_indicies = malloc((width) * sizeof(size_t));
-		if(desired_indicies == NULL) 
+		if(desired_indicies == NULL) {
+			fprintf(stderr, "%s\n", strerror(errno));
 			exit(EXIT_FAILURE);
+		}
 		num_desired_indicies = load_specific_mers_from_file(mer_fn, kmer, width, desired_indicies);
 		if(num_desired_indicies == 0) {
 			fprintf(stderr, "Error: no mers loaded from file"); 
@@ -142,8 +144,10 @@ int main(int argc, char **argv) {
 
 
 	unsigned long long *counts = malloc((width+ 1) * sizeof(unsigned long long));
-	if(counts == NULL) 
+	if(counts == NULL)  {
+		fprintf(stderr, "%s\n", strerror(errno));
 		exit(EXIT_FAILURE);
+	}
 
 	unsigned long long sequence = 0;
 	while ((read = getdelim(&line, &len, '>', fh)) != -1) {
@@ -197,11 +201,11 @@ int main(int argc, char **argv) {
 		sequence++;
 	}
 
-free(counts);
-free(line);
-free(desired_indicies);
-fclose(fh);
+	free(counts);
+	free(line);
+	free(desired_indicies);
+	fclose(fh);
 
 
-return EXIT_SUCCESS;
+	return EXIT_SUCCESS;
 }
diff --git a/kmer_utils.c b/kmer_utils.c
index 060e311..81b1e91 100644
--- a/kmer_utils.c
+++ b/kmer_utils.c
@@ -99,8 +99,10 @@ char *index_to_kmer(unsigned long long index, long kmer)  {
 	size_t j = 0;
 	char *num_array = calloc(kmer,  sizeof(char));
 	char *ret = calloc(kmer + 1, sizeof(char));
-	if(ret == NULL)
+	if(ret == NULL || num_array == NULL) {
+		fprintf(stderr, "%s\n", strerror(errno));
 		exit(EXIT_FAILURE);
+	}
 		
 
 	// this is the core of the conversion. modulus 4 for base 4 conversion
@@ -172,7 +174,7 @@ unsigned long long * get_kmer_counts_from_file(FILE *fh, const unsigned int kmer
 	// malloc our return array
 	unsigned long long * counts = calloc((width+ 1), sizeof(unsigned long long));
 	if(counts == NULL)  {
-		fprintf(stderr, strerror(errno));
+		fprintf(stderr, "%s\n", strerror(errno));
 		exit(EXIT_FAILURE);
 	}
 
@@ -234,7 +236,7 @@ unsigned long long * get_kmer_counts_from_filename(const char *fn, const unsigne
 		FILE *fh = fopen(fn, "r");
 		if(fh == NULL) {
 			fprintf(stderr, "Could not open %s - %s\n", fn, strerror(errno));
-			return 0;
+			return NULL;
 		}
 
 		return get_kmer_counts_from_file(fh, kmer);
-- 
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