From 510a8001307afc24199d22bbfb7730c972ca6d69 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Mon, 11 Nov 2013 19:42:48 -0500
Subject: fix warnings

---
 kmer_total_count.c | 35 +++++++++++++++++++++--------------
 kmer_utils.h       |  1 +
 2 files changed, 22 insertions(+), 14 deletions(-)

diff --git a/kmer_total_count.c b/kmer_total_count.c
index 8310e00..57d4fcc 100644
--- a/kmer_total_count.c
+++ b/kmer_total_count.c
@@ -13,7 +13,7 @@ int main(int argc, char **argv) {
 
 	char *filename = NULL;
 
-	unsigned int kmer = NULL;
+	unsigned int kmer = 0;
 
 	bool nonzero = 0;
 	bool label = 0;
@@ -21,9 +21,7 @@ int main(int argc, char **argv) {
 
 	unsigned long long width = 0;
 
-  unsigned long long i = 0;
-
-  long long j = 0;
+	unsigned long long i = 0;
 
 	static struct option long_options[] = {
 		{"input", required_argument, 0, 'i'},
@@ -69,7 +67,7 @@ int main(int argc, char **argv) {
 		fprintf(stderr, "Error: filename (-i) must be supplied\n");
 		exit(EXIT_FAILURE);
 	}
-	if(kmer == NULL && !kmer_set) {
+	if(kmer == 0 && !kmer_set) {
 		fprintf(stderr, "Error: kmer (-k) must be supplied\n");
 		exit(EXIT_FAILURE);
 	}
@@ -87,26 +85,35 @@ int main(int argc, char **argv) {
 		// if labels is set, print out our labels
 		if(label) {
 			for(i = 0; i < width; i++)
-				if(counts[i] != 0) 
-					fprintf(stdout, "%s\t%llu\n", index_to_kmer(i, kmer), counts[i]);
-				
+				if(counts[i] != 0) {
+					char *kmer_str = index_to_kmer(i, kmer);
+					fprintf(stdout, "%s\t%llu\n", kmer_str, counts[i]);
+					free(kmer_str);
+				}
+
 		}
 		else {
 			for(i = 0; i < width; i++)
 				if(counts[i] != 0) 
 					fprintf(stdout, "%llu\t%llu\n", i, counts[i]);
-				
+
 		}
 	}
 	// If we aren't printing nonzeros print everything
 	else {
 		if(label) {
-			for(i = 0; i < width; i++)
-				fprintf(stdout, "%s\t%llu\n", index_to_kmer(i, kmer), counts[i]);
-		} 
+			for(i = 0; i < width; i++) {
+				if(counts[i] != 0) {
+					char *kmer_str = index_to_kmer(i, kmer);
+					fprintf(stdout, "%s\t%llu\n", kmer_str, counts[i]);
+					free(kmer_str);
+				}
+			} 
+		}
 		else {
-		for(i = 0; i < width; i=i+4)
-			fprintf(stdout, "%llu\n%llu\n%llu\n%llu\n", counts[i], counts[i+1], counts[i+2], counts[i+3]);
+			for(i = 0; i < width; i=i+4) {
+				fprintf(stdout, "%llu\n%llu\n%llu\n%llu\n", counts[i], counts[i+1], counts[i+2], counts[i+3]);
+			}
 		}
 	}
 	return EXIT_SUCCESS;
diff --git a/kmer_utils.h b/kmer_utils.h
index 4ed5928..762c20c 100644
--- a/kmer_utils.h
+++ b/kmer_utils.h
@@ -1,6 +1,7 @@
 // Kmer functions
 void convert_kmer_to_num(char *str, const unsigned long length);
 unsigned long num_to_index(const char *str, const int kmer, const long error_pos);
+char *index_to_kmer(unsigned long long index, long kmer);
 unsigned long long * get_kmer_counts_from_file(const char *fn, const int kmer);
 
 // Utility functions
-- 
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