performance boost from skipping our first newline. It seems crazy, but this could be up to a 10-15% improvement because of our strstrip function. Each time we were copying the entire array, even if we didn't need to. There will be more of a benefit on a single line'd sequence file, but will see a speed up on all

1 files changed, 5 insertions, 1 deletions

diff --git a/kmer_utils.c b/kmer_utils.c
index ef46842..dc79700 100644
--- a/kmer_utils.c
+++ b/kmer_utils.c
@@ -82,7 +82,7 @@ char *index_to_kmer(unsigned long long index, long kmer)  {
 
 	// reverse the array, as j increases, decrease i
 	for(j = 0; j < start; j++, i--) 
-		ret[j + offset] = reverse_alpha[num_array[i]];
+		ret[j + offset] = reverse_alpha[(int)num_array[i]];
 	
   // set our last character to the null termination byte
 	ret[kmer + 1] = '\0';
@@ -151,6 +151,9 @@ unsigned long long * get_kmer_counts_from_file(const char *fn, const unsigned in
 		if(start == NULL) 
 			continue;
 
+		// point to one past that.
+		start = start + 1;
+
 		size_t start_len = strlen(start);
 
 
@@ -163,6 +166,7 @@ unsigned long long * get_kmer_counts_from_file(const char *fn, const unsigned in
 			}
 		}
 
+
 		// strip out all other newlines to handle multiline sequences
 		str = strnstrip(start, str, '\n',start_len);
 		size_t seq_length = strlen(str);