File: NucConversion.cpp

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#include <pbdata/NucConversion.hpp>

int TwoBit[] = {
    0,   1,   2,   3,   0,   1,   2,   3,   255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 0,   255, 1,   255, 255, 255, 2,   255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 3,   255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 0,   255, 1,   255, 255, 255, 2,   255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 3,   255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255};

//
// Map from charcter to 3 bit.  Treat all non ACGT IUPAC as N
// IPUAC: ACGT U M R W S Y K V H D N
//

int ThreeBit[] = {
    0, 1, 2, 3, 4, 255, 255, 255,            // 0..3 are native nucletides, 4
                                             // is an 'N', which is
                                             // represented just fine in the 3
                                             // bit mode.
    255, 255, 255, 255, 255, 255, 255, 255,  // 8
    255, 255, 255, 255, 255, 255, 255, 255,  // 16
    255, 255, 255, 255, 255, 255, 255, 255,  // 24
    255, 255, 255, 255, 5, 255, 255, 255,    // 32  define '$' for bwt.
    255, 255, 255, 255, 255, 255, 255, 255,  // 40
    255, 255, 255, 255, 255, 255, 255, 255,  // 48
    255, 255, 255, 255, 255, 255, 255, 255,  // 56
    255, 0, 4, 1, 4, 255, 255, 2,            // 64
    4, 255, 255, 4, 255, 4, 4, 255,          // 72
    255, 255, 4, 4, 3, 4, 4, 4,              // 80
    255, 4, 255, 255, 255, 255, 255, 4,      // 88
    255, 0, 4, 1, 4, 255, 255, 2,            // 96
    4, 255, 255, 4, 255, 4, 4, 255,          // 104
    255, 255, 4, 4, 3, 4, 4, 4,              // 112
    4, 4, 255, 255, 255, 255, 255, 255,      // 120
    255, 255, 255, 255, 255, 255, 255, 255,  // 128
    255, 255, 255, 255, 255, 255, 255, 255,  // 136
    255, 255, 255, 255, 255, 255, 255, 255,  // 144
    255, 255, 255, 255, 255, 255, 255, 255,  // 152
    255, 255, 255, 255, 255, 255, 255, 255,  // 160
    255, 255, 255, 255, 255, 255, 255, 255,  // 168
    255, 255, 255, 255, 255, 255, 255, 255,  // 176
    255, 255, 255, 255, 255, 255, 255, 255,  // 184
    255, 255, 255, 255, 255, 255, 255, 255,  // 192
    255, 255, 255, 255, 255, 255, 255, 255,  // 200
    255, 255, 255, 255, 255, 255, 255, 255,  // 208
    255, 255, 255, 255, 255, 255, 255, 255,  // 216
    255, 255, 255, 255, 255, 255, 255, 255,  // 224
    255, 255, 255, 255, 255, 255, 255, 255,  // 232
    255, 255, 255, 255, 255, 255, 255, 255,  // 240
    255, 255, 255, 255, 255, 255, 255, 255   // 248
};

int IsACTG[] = {
    1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};

int IsLowerCase[] = {
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};

int FourBit[] = {
    0,   1,   2,   3,   4,   5,   6,   7,   255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 0,   255, 1,   255, 255, 255, 2,   255, 255, 255, 255,
    255, 255, 8,   255, 255, 255, 255, 255, 3,   255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 4,   255, 5,   255, 255, 255, 6,   255, 255, 255, 255, 255, 255, 8,   255, 255, 255,
    255, 255, 7,   255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255};

int FourBitToAscii[] = {'A', 'C', 'G', 'T', 'a', 'c', 'g', 't', 'N', 'X'};
int ThreeBitToAscii[] = {'A', 'C', 'G', 'T', 'N', '$'};

int MaskedFourBit[] = {
    9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9,
    9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9,
    9, 0, 9, 1, 9, 9, 9, 2, 9, 9, 9, 9, 9, 9, 8, 9, 9, 9, 9, 9, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9,
    9, 4, 9, 5, 9, 9, 9, 6, 9, 9, 9, 9, 9, 9, 8, 9, 9, 9, 9, 9, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9,
    9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9,
    9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9,
    9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9,
    9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9};

unsigned char AllToUpper[] = {
    'A', 'C', 'G', 'T', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'A', 'N', 'C', 'N', 'N', 'N', 'G', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'T', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'A', 'N', 'C', 'N', 'N', 'N', 'G', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'T', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N'};
char AllToLower[] = {
    'a', 'c', 'g', 't', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'a', 'N', 'c', 'N', 'N', 'N', 'g', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 't', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'a', 'N', 'c', 'N', 'N', 'N', 'g', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 't', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
    'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N'};

unsigned char PreserveCase[] = {
    0,   1,   2,   3,   4,   5,   6,   7,   8,   9,   10,  11,  12,  13,  14,  15,  16,  17,  18,
    19,  20,  21,  22,  23,  24,  25,  26,  27,  28,  29,  30,  31,  32,  33,  34,  35,  36,  37,
    38,  39,  40,  41,  42,  43,  44,  45,  46,  47,  48,  49,  50,  51,  52,  53,  54,  55,  56,
    57,  58,  59,  60,  61,  62,  63,  64,  65,  66,  67,  68,  69,  70,  71,  72,  73,  74,  75,
    76,  77,  78,  79,  80,  81,  82,  83,  84,  85,  86,  87,  88,  89,  90,  91,  92,  93,  94,
    95,  96,  97,  98,  99,  100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113,
    114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,
    133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151,
    152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170,
    171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189,
    190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208,
    209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227,
    228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246,
    247, 248, 249, 250, 251, 252, 253, 254, 255};

char TwoBitToAscii[] = {'A', 'C', 'G', 'T'};

unsigned char ReverseComplementNuc[] = {
    3,   2,   1,   0,   127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127, 'T', 127, 'G', 127, 127, 127, 'C', 127, 127, 127, 127,
    127, 127, 'N', 127, 127, 127, 127, 127, 'A', 127, 127, 127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 't', 127, 'g', 127, 127, 127, 'c', 127, 127, 127, 127, 127, 127, 'n', 127, 127, 127,
    127, 127, 'a', 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127, 127};

//
// HDF Column Orders: GTAC
// A - column 2; C - column 3;
// G - column 0; T - column 1;
// Ascii code:
// A=65, C=67, G=71,  T=84
// a=97, c=99, g=116, t=103
//
int NucToHdfColumnOrder[] = {
    2,   3,   1,   0,   2,   3,   1,   0,   255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 2,   255, 3,   255, 255, 255, 1,   255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 0,   255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 2,   255, 3,   255, 255, 255, 1,   255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 0,   255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255,
    255, 255, 255, 255, 255, 255, 255, 255, 255};