From 87044b41d8fc83220010e51a126377333f1af24a Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Fri, 20 Nov 2015 11:32:47 +0100
Subject: [PATCH] modified the encoding function on 2 bits a little

---
 src/encode.c | 24 +++++++++++++++---------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/src/encode.c b/src/encode.c
index 29f06a1..80b1350 100644
--- a/src/encode.c
+++ b/src/encode.c
@@ -53,51 +53,52 @@ bool only_ATGC(char* seq)
 }
 
 
-byte_t* encode_seq_on_2_bits(char* seq, int32_t length)		// TODO shift = 2
+byte_t* encode_seq_on_2_bits(char* seq, int32_t length)
 {
 	byte_t*  seq_b;
-	uint8_t  shift;
+	uint8_t  modulo;
 	int32_t  length_b;
 	int32_t   i;
 
 //	fprintf(stderr, "\n>>>>>>>>>>>>>>>>>>Encoding sequence %s", seq);
 
 	length_b = ceil((double) length / (double) 4.0);
-
 //	fprintf(stderr, "\nLength: %d", length_b);
 
 	seq_b = (byte_t*) malloc(length_b * sizeof(byte_t));
 
+	// Initialize all the bits to 0
 	memset(seq_b, 0, length_b);
 
 	for (i=0; i<length; i++)
 	{
-		shift = 6 - 2*(i%4);
-//		fprintf(stderr, "\nshift: %u", shift);
+		// Shift of 2 to make place for new nucleotide
+		seq_b[i/4] <<= 2;
 
+		// Add new nucleotide
 		switch (seq[i])
 		{
 		case 'a':
 		case 'A':
-			seq_b[i/4] |= NUC_A << shift;
+			seq_b[i/4] |= NUC_A;
 //			fprintf(stderr, "\nIn byte %d, writing A:", i/4);
 //			print_bits(seq_b, length_b);
 			break;
 		case 'c':
 		case 'C':
-			seq_b[i/4] |= NUC_C << shift;
+			seq_b[i/4] |= NUC_C;
 //			fprintf(stderr, "\nIn byte %d, writing C:", i/4);
 //			print_bits(seq_b, length_b);
 			break;
 		case 'g':
 		case 'G':
-			seq_b[i/4] |= NUC_G << shift;
+			seq_b[i/4] |= NUC_G;
 //			fprintf(stderr, "\nIn byte %d, writing G:", i/4);
 //			print_bits(seq_b, length_b);
 			break;
 		case 't':
 		case 'T':
-			seq_b[i/4] |= NUC_T << shift;
+			seq_b[i/4] |= NUC_T;
 //			fprintf(stderr, "\nIn byte %d, writing T:", i/4);
 //			print_bits(seq_b, length_b);
 			break;
@@ -107,6 +108,11 @@ byte_t* encode_seq_on_2_bits(char* seq, int32_t length)		// TODO shift = 2
 		}
 	}
 
+	// Final shift for the last byte if needed
+	modulo = (length % 4);
+	if (modulo)
+		seq_b[(i-1)/4] <<= (2*(4 - modulo));
+
 //	fprintf(stderr, "\n>>>>>>>>>Encoded:");
 //	print_bits(seq_b, length_b);