C: Added a function to get a nucleotide at a specific index in an

encoded sequence

src/encode.c

@@ -114,6 +114,35 @@ bool is_a_DNA_seq(const char* seq)
 }
 
 
+byte_t get_nucleotide_from_encoded_seq(byte_t* seq, int32_t idx, uint8_t encoding)
+{
+	uint8_t shift;
+	uint8_t mask;
+	byte_t  nuc;
+
+	if (encoding == 2)
+	{
+		shift = 6 - 2*(idx % 4);
+		mask = NUC_MASK_2B << shift;
+		nuc = (seq[idx/4] & mask) >> shift;
+	}
+	else if (encoding == 4)
+	{
+		shift = 4 - 4*(idx % 2);
+		mask = NUC_MASK_4B << shift;
+		nuc = (seq[idx/2] & mask) >> shift;
+	}
+	else
+	{
+		obi_set_errno(OBI_DECODE_ERROR);
+		obidebug(1, "\nInvalid encoding base: must be on 2 bits or 4 bits");
+		return -1;
+	}
+
+	return nuc;
+}
+
+
 byte_t* encode_seq_on_2_bits(const char* seq, int32_t length)
 {
 	byte_t*  seq_b;
@@ -405,6 +434,7 @@ char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq)
 
 ///////////////////// FOR DEBUGGING ///////////////////////////
 //NOTE: The first byte is printed the first (at the left-most).
+// TODO Move to utils
 
 void print_bits(void* ptr, int32_t size)
 {

src/encode.h

@@ -108,6 +108,24 @@ bool only_IUPAC_DNA(const char* seq);
 bool is_a_DNA_seq(const char* seq);
 
 
+/**
+ * @brief Returns a nucleotide from a DNA sequence encoded
+ *        with each nucleotide on 2 or 4 bits.
+ *
+ * @param seq The encoded sequence.
+ * @param idx The index (in the decoded sequence) of the nucleotide to get.
+ * @param encoding An integer indicating whether the sequence is encoded with each nucleotide on 2 or 4 bits.
+ *
+ * @returns The (still encoded) nucleotide at the given index.
+ * @retval 255 if an error occurred.
+ *
+ * @see decode_seq_on_2_bits() and decode_seq_on_4_bits()
+ * @since January 2019
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+byte_t get_nucleotide_from_encoded_seq(byte_t* seq, int32_t idx, uint8_t encoding);
+
+
 /**
  * @brief Encodes a DNA sequence with each nucleotide coded on 2 bits.
  *