New column type for DNA sequences. Only for those coded on 2 bits (only

'ATGCatgc') for now.

src/encode.h

@@ -0,0 +1,95 @@
+/****************************************************************************
+ * Encoding header file	                                                    *
+ ****************************************************************************/
+
+/**
+ * @file encode.h
+ * @author Celine Mercier
+ * @date November 18th 2015
+ * @brief Header file for encoding DNA sequences.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <stdbool.h>
+
+#include "obiarray.h"
+
+
+#define NUC_MASK 0x3   /**< Binary: 11 to use when decoding */
+
+
+/**
+ * @brief enum for the 2-bits codes for each of the 4 nucleotides.
+ */
+enum
+{
+    NUC_A = 0x0,   /* binary: 00 */
+    NUC_C = 0x1,   /* binary: 01 */
+    NUC_G = 0x2,   /* binary: 10 */
+    NUC_T = 0x3,   /* binary: 11 */
+};
+
+
+/**
+ * @brief Checks if there are only 'atgcATGC' characters in a
+ *        character string.
+ *
+ * @param seq The sequence to check.
+ *
+ * @returns A boolean value indicating if there are only
+ *          'atgcATGC' characters in a character string.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+bool only_ATGC(char* seq);
+
+
+/**
+ * @brief Encodes a DNA sequence with each nucleotide coded on 2 bits.
+ *
+ *    A or a : 00
+ *    C or c : 01
+ *    T or t : 10
+ *    G or g : 11
+ *
+ * @warning The DNA sequence must contain only 'atgcATGC' characters.
+ *
+ * @param seq The sequence to encode.
+ * @param length The length of the sequence to encode.
+ *
+ * @returns The encoded sequence.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+byte_t* encode_seq_on_2_bits(char* seq, int32_t length);
+
+
+/**
+ * @brief Decodes a DNA sequence that is coded with each nucleotide on 2 bits.
+ *
+ *    A or a : 00
+ *    C or c : 01
+ *    T or t : 10
+ *    G or g : 11
+ *
+ * @param seq The sequence to decode.
+ * @param length_seq The initial length of the sequence before it was encoded.
+ *
+ * @returns The decoded sequence ended with '\0'.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq);
+
+
+////////// FOR DEBUGGING ///////////
+
+// little endian
+void print_bits(void* ptr, int32_t length);
+