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1 // ***************************************************************************
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2 // BamConstants.h (c) 2011 Derek Barnett
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3 // Marth Lab, Department of Biology, Boston College
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4 // All rights reserved.
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5 // ---------------------------------------------------------------------------
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6 // Last modified: 19 April 2011 (DB)
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7 // ---------------------------------------------------------------------------
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8 // Provides basic constants for handling BAM files.
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9 // ***************************************************************************
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10
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11 #ifndef BAM_CONSTANTS_H
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12 #define BAM_CONSTANTS_H
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13
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14 #include <string>
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15
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16 /*! \namespace BamTools::Constants
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17 \brief Provides basic constants for handling BAM files.
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18 */
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19
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20 namespace BamTools {
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21 namespace Constants {
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22
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23 const int BAM_SIZEOF_INT = 4;
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24
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25 // header magic number
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26 const char* const BAM_HEADER_MAGIC = "BAM\1";
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27 const unsigned int BAM_HEADER_MAGIC_LENGTH = 4;
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28
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29 // BAM alignment core size
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30 const int BAM_CORE_SIZE = 32;
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31 const int BAM_CORE_BUFFER_SIZE = 8;
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32
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33 // BAM alignment flags
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34 const int BAM_ALIGNMENT_PAIRED = 0x0001;
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35 const int BAM_ALIGNMENT_PROPER_PAIR = 0x0002;
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36 const int BAM_ALIGNMENT_UNMAPPED = 0x0004;
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37 const int BAM_ALIGNMENT_MATE_UNMAPPED = 0x0008;
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38 const int BAM_ALIGNMENT_REVERSE_STRAND = 0x0010;
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39 const int BAM_ALIGNMENT_MATE_REVERSE_STRAND = 0x0020;
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40 const int BAM_ALIGNMENT_READ_1 = 0x0040;
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41 const int BAM_ALIGNMENT_READ_2 = 0x0080;
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42 const int BAM_ALIGNMENT_SECONDARY = 0x0100;
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43 const int BAM_ALIGNMENT_QC_FAILED = 0x0200;
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44 const int BAM_ALIGNMENT_DUPLICATE = 0x0400;
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45
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46 // CIGAR constants
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47 const char* const BAM_CIGAR_LOOKUP = "MIDNSHP=X";
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48 const int BAM_CIGAR_MATCH = 0;
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49 const int BAM_CIGAR_INS = 1;
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50 const int BAM_CIGAR_DEL = 2;
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51 const int BAM_CIGAR_REFSKIP = 3;
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52 const int BAM_CIGAR_SOFTCLIP = 4;
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53 const int BAM_CIGAR_HARDCLIP = 5;
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54 const int BAM_CIGAR_PAD = 6;
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55 const int BAM_CIGAR_SEQMATCH = 7;
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56 const int BAM_CIGAR_MISMATCH = 8;
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57
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58 const char BAM_CIGAR_MATCH_CHAR = 'M';
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59 const char BAM_CIGAR_INS_CHAR = 'I';
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60 const char BAM_CIGAR_DEL_CHAR = 'D';
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61 const char BAM_CIGAR_REFSKIP_CHAR = 'N';
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62 const char BAM_CIGAR_SOFTCLIP_CHAR = 'S';
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63 const char BAM_CIGAR_HARDCLIP_CHAR = 'H';
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64 const char BAM_CIGAR_PAD_CHAR = 'P';
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65 const char BAM_CIGAR_SEQMATCH_CHAR = '=';
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66 const char BAM_CIGAR_MISMATCH_CHAR = 'X';
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67
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68 const int BAM_CIGAR_SHIFT = 4;
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69 const int BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1);
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70
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71 // BAM tag types
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72 const char BAM_TAG_TYPE_ASCII = 'A';
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73 const char BAM_TAG_TYPE_UINT8 = 'c';
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74 const char BAM_TAG_TYPE_INT8 = 'C';
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75 const char BAM_TAG_TYPE_UINT16 = 's';
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76 const char BAM_TAG_TYPE_INT16 = 'S';
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77 const char BAM_TAG_TYPE_UINT32 = 'i';
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78 const char BAM_TAG_TYPE_INT32 = 'I';
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79 const char BAM_TAG_TYPE_FLOAT = 'f';
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80 const char BAM_TAG_TYPE_STRING = 'Z';
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81 const char BAM_TAG_TYPE_HEX = 'H';
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82 const char BAM_TAG_TYPE_ARRAY = 'B';
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83
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84 const size_t BAM_TAG_TAGSIZE = 2;
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85 const size_t BAM_TAG_TYPESIZE = 1;
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86 const int BAM_TAG_ARRAYBASE_SIZE = 8;
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87
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88 // DNA bases
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89 const char* const BAM_DNA_LOOKUP = "=ACMGRSVTWYHKDBN";
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90 const unsigned char BAM_BASECODE_EQUAL = 0;
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91 const unsigned char BAM_BASECODE_A = 1;
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92 const unsigned char BAM_BASECODE_C = 2;
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93 const unsigned char BAM_BASECODE_G = 4;
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94 const unsigned char BAM_BASECODE_T = 8;
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95 const unsigned char BAM_BASECODE_N = 15;
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96
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97 const char BAM_DNA_EQUAL = '=';
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98 const char BAM_DNA_A = 'A';
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99 const char BAM_DNA_C = 'C';
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100 const char BAM_DNA_G = 'G';
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101 const char BAM_DNA_T = 'T';
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102 const char BAM_DNA_N = 'N';
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103 const char BAM_DNA_DEL = '-';
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104 const char BAM_DNA_PAD = '*';
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105
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106 // zlib constants
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107 const int GZIP_ID1 = 31;
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108 const int GZIP_ID2 = 139;
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109 const int CM_DEFLATE = 8;
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110 const int FLG_FEXTRA = 4;
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111 const int OS_UNKNOWN = 255;
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112 const int BGZF_XLEN = 6;
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113 const int BGZF_ID1 = 66;
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114 const int BGZF_ID2 = 67;
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115 const int BGZF_LEN = 2;
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116 const int GZIP_WINDOW_BITS = -15;
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117 const int Z_DEFAULT_MEM_LEVEL = 8;
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118
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119 // BZGF constants
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120 const int BGZF_BLOCK_HEADER_LENGTH = 18;
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121 const int BGZF_BLOCK_FOOTER_LENGTH = 8;
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122 const int BGZF_MAX_BLOCK_SIZE = 65536;
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123 const int BGZF_DEFAULT_BLOCK_SIZE = 65536;
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124
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125 } // namespace Constants
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126 } // namespace BamTools
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127
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128 #endif // BAM_CONSTANTS_H
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