From c7b8db6a2e07a4827c00d6f9804ab36eb47ed088 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Thu, 21 Apr 2016 13:45:39 +0200
Subject: [PATCH] Replaced malloc+memset with calloc

---
 src/encode.c | 26 ++++++++++----------------
 1 file changed, 10 insertions(+), 16 deletions(-)

diff --git a/src/encode.c b/src/encode.c
index 6faebc2..0611b8f 100644
--- a/src/encode.c
+++ b/src/encode.c
@@ -63,17 +63,14 @@ byte_t* encode_seq_on_2_bits(const char* seq, int32_t length)
 
 	length_b = ceil((double) length / (double) 4.0);
 
-	seq_b = (byte_t*) malloc(length_b * sizeof(byte_t));
+	seq_b = (byte_t*) calloc(length_b, sizeof(byte_t));
 	if (seq_b == NULL)
 	{
-		obi_set_errno(OBI_MALLOC_ERROR);		// TODO
+		obi_set_errno(OBI_MALLOC_ERROR);
 		obidebug(1, "\nError allocating memory for an encoded DNA sequence");
 		return NULL;
 	}
 
-	// Initialize all the bits to 0
-	memset(seq_b, 0, length_b);
-
 	for (i=0; i<length; i++)
 	{
 		// Shift of 2 to make place for new nucleotide
@@ -99,7 +96,7 @@ byte_t* encode_seq_on_2_bits(const char* seq, int32_t length)
 			seq_b[i/4] |= NUC_T_2b;
 			break;
 		default:
-			obi_set_errno(OBI_ENCODE_ERROR);		// TODO
+			obi_set_errno(OBI_ENCODE_ERROR);
 			obidebug(1, "\nInvalid nucleotide base when encoding (not [atgcATGC])");
 			return NULL;
 		}
@@ -125,7 +122,7 @@ char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq)
 	seq = (char*) malloc((length_seq+1) * sizeof(char));
 	if (seq == NULL)
 	{
-		obi_set_errno(OBI_MALLOC_ERROR);		// TODO
+		obi_set_errno(OBI_MALLOC_ERROR);
 		obidebug(1, "\nError allocating memory for a decoded DNA sequence");
 		return NULL;
 	}
@@ -151,7 +148,7 @@ char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq)
 			seq[i] = 't';
 			break;
 		default:
-			obi_set_errno(OBI_DECODE_ERROR);		// TODO
+			obi_set_errno(OBI_DECODE_ERROR);
 			obidebug(1, "\nInvalid nucleotide base when decoding");
 			return NULL;
 		}
@@ -172,17 +169,14 @@ byte_t* encode_seq_on_4_bits(const char* seq, int32_t length)
 
 	length_b = ceil((double) length / (double) 2.0);
 
-	seq_b = (byte_t*) malloc(length_b * sizeof(byte_t));
+	seq_b = (byte_t*) calloc(length_b, sizeof(byte_t));
 	if (seq_b == NULL)
 	{
-		obi_set_errno(OBI_MALLOC_ERROR);		// TODO
+		obi_set_errno(OBI_MALLOC_ERROR);
 		obidebug(1, "\nError allocating memory for an encoded DNA sequence");
 		return NULL;
 	}
 
-	// Initialize all the bits to 0
-	memset(seq_b, 0, length_b);
-
 	for (i=0; i<length; i++)
 	{
 		// Shift of 4 to make place for new nucleotide
@@ -252,7 +246,7 @@ byte_t* encode_seq_on_4_bits(const char* seq, int32_t length)
 			seq_b[i/2] |= NUC_N_4b;
 			break;
 		default:
-			obi_set_errno(OBI_ENCODE_ERROR);	// TODO
+			obi_set_errno(OBI_ENCODE_ERROR);
 			obidebug(1, "\nInvalid nucleotide base when encoding (not IUPAC)");
 			return NULL;
 		}
@@ -278,7 +272,7 @@ char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq)
 	seq = (char*) malloc((length_seq+1) * sizeof(char));
 	if (seq == NULL)
 	{
-		obi_set_errno(OBI_MALLOC_ERROR);		// TODO
+		obi_set_errno(OBI_MALLOC_ERROR);
 		obidebug(1, "\nError allocating memory for a decoded DNA sequence");
 		return NULL;
 	}
@@ -337,7 +331,7 @@ char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq)
 			seq[i] = 'n';
 			break;
 		default:
-			obi_set_errno(OBI_DECODE_ERROR);	// TODO
+			obi_set_errno(OBI_DECODE_ERROR);
 			obidebug(1, "\nInvalid nucleotide base when decoding");
 			return NULL;
 		}