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 // ***************************************************************************
11 #ifndef SAM_CONSTANTS_H
12 #define SAM_CONSTANTS_H
14 #include <api/api_global.h>
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";
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";
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";
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";
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";
61 const std::string SAM_CO_BEGIN_TOKEN = "@CO";
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";
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";
74 const unsigned int SAM_SQ_LENGTH_MIN = 1;
75 const unsigned int SAM_SQ_LENGTH_MAX = 536870911; // 2^29 - 1
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";
86 const std::string SAM_RG_SEQTECHNOLOGY_HELICOS_LOWER = "helicos";
87 const std::string SAM_RG_SEQTECHNOLOGY_HELICOS_UPPER = "HELICOS";
90 const std::string SAM_RG_SEQTECHNOLOGY_ILLUMINA_LOWER = "illumina";
91 const std::string SAM_RG_SEQTECHNOLOGY_ILLUMINA_UPPER = "ILLUMINA";
94 const std::string SAM_RG_SEQTECHNOLOGY_PACBIO_LOWER = "pacbio";
95 const std::string SAM_RG_SEQTECHNOLOGY_PACBIO_UPPER = "PACBIO";
98 const std::string SAM_RG_SEQTECHNOLOGY_SOLID_LOWER = "solid";
99 const std::string SAM_RG_SEQTECHNOLOGY_SOLID_UPPER = "SOLID";
101 } // namespace Constants
102 } // namespace BamTools
104 #endif // SAM_CONSTANTS_H