From 59ff0a86e855cd78628af40ade8b2e096eb8833e Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Tue, 7 Jan 2014 16:01:25 -0500
Subject: fix kmer_counts_per_sequence, make sure we convert the array fully,
 and update kmer_utils for str[i] == 5 instead of >> 2

---
 kmer_counts_per_sequence.c | 2 +-
 kmer_utils.c               | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/kmer_counts_per_sequence.c b/kmer_counts_per_sequence.c
index 66accc8..fceb17e 100644
--- a/kmer_counts_per_sequence.c
+++ b/kmer_counts_per_sequence.c
@@ -45,7 +45,7 @@ int main(int argc, char **argv) {
 			// reset our count matrix to zero
 			memset(counts, 0, width * sizeof(unsigned long long));
 
-			for(i = 0; i < read - kmer; i++) {
+			for(i = 0; i < read; i++) {
 				line[i] = alpha[(int)line[i]];
 			}
 
diff --git a/kmer_utils.c b/kmer_utils.c
index dc79700..2b3ce67 100644
--- a/kmer_utils.c
+++ b/kmer_utils.c
@@ -34,7 +34,7 @@ inline unsigned long num_to_index(const char *str, const int kmer, const long er
 
   for(i = kmer - 1; i >= 0; i--){
 
-		if(str[i] >> 2) { 
+		if(str[i] == 5) { 
 			#ifndef SHARED
 			position += i;
 			#endif
-- 
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