#include uint8_t dna4Cat[] = { /* 0 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 16 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 32 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, /* - */ /* 48 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 64 */ 0, 1, 2, 1, 2, 0, 0, 1, 2, 0, 0, 2, 0, 2, 2, 0, /* A B C D G H K M N */ /* 80 */ 0, 0, 2, 2, 1, 0, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, /* R S T V W X Y */ /* 96 */ 0, 1, 2, 1, 2, 0, 0, 1, 2, 0, 0, 2, 0, 2, 2, 0, /* a b c d g h k m n */ /* 112 */ 0, 0, 2, 2, 1, 0, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, /* r s t v w x y */ /* 128 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 144 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 160 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 176 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 192 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 208 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 224 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 240 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, }; /// For converting from ASCII to the Dna5 code where A=0, C=1, G=2, /// T=3, N=4 uint8_t charToDna5[] = { /* 0 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 16 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 32 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 48 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 64 */ 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 4, 0, /* A C G N */ /* 80 */ 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* T */ /* 96 */ 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 4, 0, /* a c g n */ /* 112 */ 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* t */ /* 128 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 144 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 160 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 176 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 192 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 208 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 224 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 240 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, }; /// For converting from ASCII to the reverse-complement Dna5 code where /// A=3, C=2, G=1, T=0, N=4 uint8_t rcCharToDna5[] = { /* 0 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 16 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 32 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 48 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 64 */ 0, 3, 0, 2, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 4, 0, /* A C G N */ /* 80 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* T */ /* 96 */ 0, 3, 0, 2, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 4, 0, /* a c g n */ /* 112 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* t */ /* 128 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 144 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 160 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 176 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 192 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 208 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 224 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 240 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, }; /// For converting from ASCII to the Dna5 code where A=0, C=1, G=2, /// T=3, N=4 uint8_t asc2col[] = { /* 0 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 16 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 32 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 4, 0, /* - . */ /* 48 */ 0, 1, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 0 1 2 3 */ /* 64 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 80 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 96 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 112 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 128 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 144 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 160 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 176 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 192 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 208 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 224 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 240 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, }; /** * Mapping from ASCII characters to DNA categories: * * 0 = invalid - error * 1 = DNA * 2 = IUPAC (ambiguous DNA) * 3 = not an error, but unmatchable; alignments containing this * character are invalid */ uint8_t asc2dnacat[] = { /* 0 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 16 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 32 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, /* - */ /* 48 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 64 */ 0, 1, 2, 1, 2, 0, 0, 1, 2, 0, 0, 2, 0, 2, 2, 0, /* A B C D G H K M N */ /* 80 */ 0, 0, 2, 2, 1, 0, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, /* R S T V W X Y */ /* 96 */ 0, 1, 2, 1, 2, 0, 0, 1, 2, 0, 0, 2, 0, 2, 2, 0, /* a b c d g h k m n */ /* 112 */ 0, 0, 2, 2, 1, 0, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, /* r s t v w x y */ /* 128 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 144 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 160 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 176 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 192 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 208 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 224 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 240 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, }; /** * Mapping from ASCII characters for ambiguous nucleotides into masks: */ uint8_t asc2dnamask[] = { /* 0 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 16 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 32 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 48 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 64 */ 0, 1,14, 2,13, 0, 0, 4,11, 0, 0,12, 0, 3,15, 0, /* A B C D G H K M N */ /* 80 */ 0, 0, 5, 6, 8, 0, 7, 9, 0,10, 0, 0, 0, 0, 0, 0, /* R S T V W Y */ /* 96 */ 0, 1,14, 2,13, 0, 0, 4,11, 0, 0,12, 0, 3,15, 0, /* a b c d g h k m n */ /* 112 */ 0, 0, 5, 6, 8, 0, 7, 9, 0,10, 0, 0, 0, 0, 0, 0, /* r s t v w y */ /* 128 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 144 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 160 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 176 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 192 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 208 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 224 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 240 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, }; /** * Mapping from ASCII characters for ambiguous nucleotides into masks: */ char asc2dnacomp[] = { /* 0 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 16 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 32 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,'-', 0, 0, /* 48 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 64 */ 0,'T','V','G','H', 0, 0,'C','D', 0, 0,'M', 0,'K','N', 0, /* A B C D G H K M N */ /* 80 */ 0, 0,'Y','S','A', 0,'B','W', 0,'R', 0, 0, 0, 0, 0, 0, /* R S T V W Y */ /* 96 */ 0,'T','V','G','H', 0, 0,'C','D', 0, 0,'M', 0,'K','N', 0, /* a b c d g h k m n */ /* 112 */ 0, 0,'Y','S','A', 0,'B','W', 0,'R', 0, 0, 0, 0, 0, 0, /* r s t v w y */ /* 128 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 144 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 160 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 176 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 192 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 208 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 224 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 240 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }; /** * Mapping from ASCII characters to color categories: * * 0 = invalid - error * 1 = valid color * 2 = IUPAC (ambiguous DNA) - there is no such thing for colors to my * knowledge * 3 = not an error, but unmatchable; alignments containing this * character are invalid */ uint8_t asc2colcat[] = { /* 0 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 16 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 32 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 3, 0, /* - . */ /* 48 */ 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 0 1 2 3 */ /* 64 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 80 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 96 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 112 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 128 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 144 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 160 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 176 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 192 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 208 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 224 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, /* 240 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, }; /** * Convert a nucleotide and a color to the paired nucleotide. Indexed * first by nucleotide then by color. Note that this is exactly the * same as the dinuc2color array. */ uint8_t nuccol2nuc[5][5] = { /* B G O R . */ /* A */ {0, 1, 2, 3, 4}, /* C */ {1, 0, 3, 2, 4}, /* G */ {2, 3, 0, 1, 4}, /* T */ {3, 2, 1, 0, 4}, /* N */ {4, 4, 4, 4, 4} }; /** * Convert a pair of nucleotides to a color. */ uint8_t dinuc2color[5][5] = { /* A */ {0, 1, 2, 3, 4}, /* C */ {1, 0, 3, 2, 4}, /* G */ {2, 3, 0, 1, 4}, /* T */ {3, 2, 1, 0, 4}, /* N */ {4, 4, 4, 4, 4} };