src/api/SamConstants.h

   1 // ***************************************************************************
   2 // SamConstants.h (c) 2010 Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Last modified: 23 December 2010 (DB)
   7 // ---------------------------------------------------------------------------
   8 // Provides constants for SAM header
   9 // ***************************************************************************
  10
  11 #ifndef SAM_CONSTANTS_H
  12 #define SAM_CONSTANTS_H
  13
  14 #include <api/api_global.h>
  15 #include <string>
  16
  17 namespace BamTools {
  18 namespace Constants {
  19
  20 const char SAM_COLON  = ':';
  21 const char SAM_EQUAL  = '=';
  22 const char SAM_PERIOD = '.';
  23 const char SAM_STAR   = '*';
  24 const char SAM_TAB    = '\t';
  25 const std::string SAM_DIGITS = "0123456789";
  26
  27 // HD entries
  28 const std::string SAM_HD_BEGIN_TOKEN    = "@HD";
  29 const std::string SAM_HD_VERSION_TAG    = "VN";
  30 const std::string SAM_HD_SORTORDER_TAG  = "SO";
  31 const std::string SAM_HD_GROUPORDER_TAG = "GO";
  32
  33 // SQ entries
  34 const std::string SAM_SQ_BEGIN_TOKEN    = "@SQ";
  35 const std::string SAM_SQ_NAME_TAG       = "SN";
  36 const std::string SAM_SQ_LENGTH_TAG     = "LN";
  37 const std::string SAM_SQ_ASSEMBLYID_TAG = "AS";
  38 const std::string SAM_SQ_URI_TAG        = "UR";
  39 const std::string SAM_SQ_CHECKSUM_TAG   = "M5";
  40 const std::string SAM_SQ_SPECIES_TAG    = "SP";
  41
  42 // RG entries
  43 const std::string SAM_RG_BEGIN_TOKEN             = "@RG";
  44 const std::string SAM_RG_ID_TAG                  = "ID";
  45 const std::string SAM_RG_SAMPLE_TAG              = "SM";
  46 const std::string SAM_RG_LIBRARY_TAG             = "LB";
  47 const std::string SAM_RG_DESCRIPTION_TAG         = "DS";
  48 const std::string SAM_RG_PLATFORMUNIT_TAG        = "PU";
  49 const std::string SAM_RG_PREDICTEDINSERTSIZE_TAG = "PI";
  50 const std::string SAM_RG_SEQCENTER_TAG           = "CN";
  51 const std::string SAM_RG_PRODUCTIONDATE_TAG      = "DT";
  52 const std::string SAM_RG_SEQTECHNOLOGY_TAG       = "PL";
  53
  54 // PG entries
  55 const std::string SAM_PG_BEGIN_TOKEN     = "@PG";
  56 const std::string SAM_PG_NAME_TAG        = "ID";
  57 const std::string SAM_PG_VERSION_TAG     = "VN";
  58 const std::string SAM_PG_COMMANDLINE_TAG = "CL";
  59
  60 // CO entries
  61 const std::string SAM_CO_BEGIN_TOKEN = "@CO";
  62
  63 // HD:SO values
  64 const std::string SAM_HD_SORTORDER_COORDINATE = "coordinate";
  65 const std::string SAM_HD_SORTORDER_QUERYNAME  = "queryname";
  66 const std::string SAM_HD_SORTORDER_UNSORTED   = "unsorted";
  67
  68 // HD:GO values
  69 const std::string SAM_HD_GROUPORDER_NONE      = "none";
  70 const std::string SAM_HD_GROUPORDER_QUERY     = "query";
  71 const std::string SAM_HD_GROUPORDER_REFERENCE = "reference";
  72
  73 // SQ:LN values
  74 const unsigned int SAM_SQ_LENGTH_MIN = 1;
  75 const unsigned int SAM_SQ_LENGTH_MAX = 536870911; // 2^29 - 1
  76
  77 // --------------
  78 // RG:PL values
  79
  80 // 454
  81 const std::string SAM_RG_SEQTECHNOLOGY_454         = "454";
  82 const std::string SAM_RG_SEQTECHNOLOGY_LS454_LOWER = "ls454";
  83 const std::string SAM_RG_SEQTECHNOLOGY_LS454_UPPER = "LS454";
  84
  85 // Helicos
  86 const std::string SAM_RG_SEQTECHNOLOGY_HELICOS_LOWER = "helicos";
  87 const std::string SAM_RG_SEQTECHNOLOGY_HELICOS_UPPER = "HELICOS";
  88
  89 // Illumina
  90 const std::string SAM_RG_SEQTECHNOLOGY_ILLUMINA_LOWER = "illumina";
  91 const std::string SAM_RG_SEQTECHNOLOGY_ILLUMINA_UPPER = "ILLUMINA";
  92
  93 // PacBio
  94 const std::string SAM_RG_SEQTECHNOLOGY_PACBIO_LOWER = "pacbio";
  95 const std::string SAM_RG_SEQTECHNOLOGY_PACBIO_UPPER = "PACBIO";
  96
  97 // SOLiD
  98 const std::string SAM_RG_SEQTECHNOLOGY_SOLID_LOWER = "solid";
  99 const std::string SAM_RG_SEQTECHNOLOGY_SOLID_UPPER = "SOLID";
 100
 101 } // namespace Constants
 102 } // namespace BamTools
 103
 104 #endif // SAM_CONSTANTS_H