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SamConstants.h
Go to the documentation of this file.
// ***************************************************************************
// SamConstants.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 27 March 2012 (DB)
// ---------------------------------------------------------------------------
// Provides constants for SAM header
// ***************************************************************************
#ifndef SAM_CONSTANTS_H
#define SAM_CONSTANTS_H
#include <string>
#include "api/api_global.h"
namespace BamTools {
namespace Constants {
// basic char constants used in SAM format
const char SAM_COLON = ':';
const char SAM_EQUAL = '=';
const char SAM_PERIOD = '.';
const char SAM_STAR = '*';
const char SAM_TAB = '\t';
const std::string SAM_DIGITS = "0123456789";
const std::string SAM_CURRENT_VERSION = "1.4";
// HD entries
const std::string SAM_HD_BEGIN_TOKEN = "@HD";
const std::string SAM_HD_VERSION_TAG = "VN";
const std::string SAM_HD_SORTORDER_TAG = "SO";
const std::string SAM_HD_GROUPORDER_TAG = "GO";
// SQ entries
const std::string SAM_SQ_BEGIN_TOKEN = "@SQ";
const std::string SAM_SQ_ASSEMBLYID_TAG = "AS";
const std::string SAM_SQ_CHECKSUM_TAG = "M5";
const std::string SAM_SQ_LENGTH_TAG = "LN";
const std::string SAM_SQ_NAME_TAG = "SN";
const std::string SAM_SQ_SPECIES_TAG = "SP";
const std::string SAM_SQ_URI_TAG = "UR";
// RG entries
const std::string SAM_RG_BEGIN_TOKEN = "@RG";
const std::string SAM_RG_DESCRIPTION_TAG = "DS";
const std::string SAM_RG_FLOWORDER_TAG = "FO";
const std::string SAM_RG_ID_TAG = "ID";
const std::string SAM_RG_KEYSEQUENCE_TAG = "KS";
const std::string SAM_RG_LIBRARY_TAG = "LB";
const std::string SAM_RG_PLATFORMUNIT_TAG = "PU";
const std::string SAM_RG_PREDICTEDINSERTSIZE_TAG = "PI";
const std::string SAM_RG_PRODUCTIONDATE_TAG = "DT";
const std::string SAM_RG_PROGRAM_TAG = "PG";
const std::string SAM_RG_SAMPLE_TAG = "SM";
const std::string SAM_RG_SEQCENTER_TAG = "CN";
const std::string SAM_RG_SEQTECHNOLOGY_TAG = "PL";
// PG entries
const std::string SAM_PG_BEGIN_TOKEN = "@PG";
const std::string SAM_PG_COMMANDLINE_TAG = "CL";
const std::string SAM_PG_ID_TAG = "ID";
const std::string SAM_PG_NAME_TAG = "PN";
const std::string SAM_PG_PREVIOUSPROGRAM_TAG = "PP";
const std::string SAM_PG_VERSION_TAG = "VN";
// CO entries
const std::string SAM_CO_BEGIN_TOKEN = "@CO";
// HD:SO values
const std::string SAM_HD_SORTORDER_COORDINATE = "coordinate";
const std::string SAM_HD_SORTORDER_QUERYNAME = "queryname";
const std::string SAM_HD_SORTORDER_UNKNOWN = "unknown";
const std::string SAM_HD_SORTORDER_UNSORTED = "unsorted";
// HD:GO values
const std::string SAM_HD_GROUPORDER_NONE = "none";
const std::string SAM_HD_GROUPORDER_QUERY = "query";
const std::string SAM_HD_GROUPORDER_REFERENCE = "reference";
// SQ:LN values
const unsigned int SAM_SQ_LENGTH_MIN = 1;
const unsigned int SAM_SQ_LENGTH_MAX = 536870911; // 2^29 - 1
// RG:PL values
const std::string SAM_RG_SEQTECHNOLOGY_CAPILLARY = "CAPILLARY";
const std::string SAM_RG_SEQTECHNOLOGY_HELICOS = "HELICOS";
const std::string SAM_RG_SEQTECHNOLOGY_ILLUMINA = "ILLUMINA";
const std::string SAM_RG_SEQTECHNOLOGY_IONTORRENT = "IONTORRENT";
const std::string SAM_RG_SEQTECHNOLOGY_LS454 = "LS454";
const std::string SAM_RG_SEQTECHNOLOGY_PACBIO = "PACBIO";
const std::string SAM_RG_SEQTECHNOLOGY_SOLID = "SOLID";
} // namespace Constants
} // namespace BamTools
#endif // SAM_CONSTANTS_H
api_global.h
BamTools::Constants
Provides basic constants for handling BAM files.
BamTools::Constants::SAM_PERIOD
const char SAM_PERIOD
Definition SamConstants.h:22
BamTools::Constants::SAM_HD_VERSION_TAG
const std::string SAM_HD_VERSION_TAG
Definition SamConstants.h:31
BamTools::Constants::SAM_CURRENT_VERSION
const std::string SAM_CURRENT_VERSION
Definition SamConstants.h:27
BamTools::Constants::SAM_HD_SORTORDER_QUERYNAME
const std::string SAM_HD_SORTORDER_QUERYNAME
Definition SamConstants.h:72
BamTools::Constants::SAM_RG_SAMPLE_TAG
const std::string SAM_RG_SAMPLE_TAG
Definition SamConstants.h:55
BamTools::Constants::SAM_PG_BEGIN_TOKEN
const std::string SAM_PG_BEGIN_TOKEN
Definition SamConstants.h:60
BamTools::Constants::SAM_HD_SORTORDER_TAG
const std::string SAM_HD_SORTORDER_TAG
Definition SamConstants.h:32
BamTools::Constants::SAM_SQ_BEGIN_TOKEN
const std::string SAM_SQ_BEGIN_TOKEN
Definition SamConstants.h:36
BamTools::Constants::SAM_PG_PREVIOUSPROGRAM_TAG
const std::string SAM_PG_PREVIOUSPROGRAM_TAG
Definition SamConstants.h:64
BamTools::Constants::SAM_HD_SORTORDER_UNSORTED
const std::string SAM_HD_SORTORDER_UNSORTED
Definition SamConstants.h:74
BamTools::Constants::SAM_SQ_LENGTH_TAG
const std::string SAM_SQ_LENGTH_TAG
Definition SamConstants.h:39
BamTools::Constants::SAM_HD_GROUPORDER_NONE
const std::string SAM_HD_GROUPORDER_NONE
Definition SamConstants.h:77
BamTools::Constants::SAM_RG_PRODUCTIONDATE_TAG
const std::string SAM_RG_PRODUCTIONDATE_TAG
Definition SamConstants.h:53
BamTools::Constants::SAM_RG_SEQTECHNOLOGY_ILLUMINA
const std::string SAM_RG_SEQTECHNOLOGY_ILLUMINA
Definition SamConstants.h:88
BamTools::Constants::SAM_RG_BEGIN_TOKEN
const std::string SAM_RG_BEGIN_TOKEN
Definition SamConstants.h:45
BamTools::Constants::SAM_COLON
const char SAM_COLON
Definition SamConstants.h:20
BamTools::Constants::SAM_SQ_NAME_TAG
const std::string SAM_SQ_NAME_TAG
Definition SamConstants.h:40
BamTools::Constants::SAM_PG_ID_TAG
const std::string SAM_PG_ID_TAG
Definition SamConstants.h:62
BamTools::Constants::SAM_RG_KEYSEQUENCE_TAG
const std::string SAM_RG_KEYSEQUENCE_TAG
Definition SamConstants.h:49
BamTools::Constants::SAM_HD_SORTORDER_UNKNOWN
const std::string SAM_HD_SORTORDER_UNKNOWN
Definition SamConstants.h:73
BamTools::Constants::SAM_RG_LIBRARY_TAG
const std::string SAM_RG_LIBRARY_TAG
Definition SamConstants.h:50
BamTools::Constants::SAM_HD_GROUPORDER_REFERENCE
const std::string SAM_HD_GROUPORDER_REFERENCE
Definition SamConstants.h:79
BamTools::Constants::SAM_HD_SORTORDER_COORDINATE
const std::string SAM_HD_SORTORDER_COORDINATE
Definition SamConstants.h:71
BamTools::Constants::SAM_RG_SEQTECHNOLOGY_HELICOS
const std::string SAM_RG_SEQTECHNOLOGY_HELICOS
Definition SamConstants.h:87
BamTools::Constants::SAM_SQ_LENGTH_MAX
const unsigned int SAM_SQ_LENGTH_MAX
Definition SamConstants.h:83
BamTools::Constants::SAM_PG_NAME_TAG
const std::string SAM_PG_NAME_TAG
Definition SamConstants.h:63
BamTools::Constants::SAM_RG_DESCRIPTION_TAG
const std::string SAM_RG_DESCRIPTION_TAG
Definition SamConstants.h:46
BamTools::Constants::SAM_RG_PREDICTEDINSERTSIZE_TAG
const std::string SAM_RG_PREDICTEDINSERTSIZE_TAG
Definition SamConstants.h:52
BamTools::Constants::SAM_RG_SEQTECHNOLOGY_TAG
const std::string SAM_RG_SEQTECHNOLOGY_TAG
Definition SamConstants.h:57
BamTools::Constants::SAM_RG_PLATFORMUNIT_TAG
const std::string SAM_RG_PLATFORMUNIT_TAG
Definition SamConstants.h:51
BamTools::Constants::SAM_DIGITS
const std::string SAM_DIGITS
Definition SamConstants.h:25
BamTools::Constants::SAM_RG_SEQTECHNOLOGY_CAPILLARY
const std::string SAM_RG_SEQTECHNOLOGY_CAPILLARY
Definition SamConstants.h:86
BamTools::Constants::SAM_HD_GROUPORDER_QUERY
const std::string SAM_HD_GROUPORDER_QUERY
Definition SamConstants.h:78
BamTools::Constants::SAM_CO_BEGIN_TOKEN
const std::string SAM_CO_BEGIN_TOKEN
Definition SamConstants.h:68
BamTools::Constants::SAM_RG_SEQTECHNOLOGY_IONTORRENT
const std::string SAM_RG_SEQTECHNOLOGY_IONTORRENT
Definition SamConstants.h:89
BamTools::Constants::SAM_RG_SEQTECHNOLOGY_PACBIO
const std::string SAM_RG_SEQTECHNOLOGY_PACBIO
Definition SamConstants.h:91
BamTools::Constants::SAM_RG_SEQCENTER_TAG
const std::string SAM_RG_SEQCENTER_TAG
Definition SamConstants.h:56
BamTools::Constants::SAM_SQ_URI_TAG
const std::string SAM_SQ_URI_TAG
Definition SamConstants.h:42
BamTools::Constants::SAM_RG_SEQTECHNOLOGY_LS454
const std::string SAM_RG_SEQTECHNOLOGY_LS454
Definition SamConstants.h:90
BamTools::Constants::SAM_RG_FLOWORDER_TAG
const std::string SAM_RG_FLOWORDER_TAG
Definition SamConstants.h:47
BamTools::Constants::SAM_PG_VERSION_TAG
const std::string SAM_PG_VERSION_TAG
Definition SamConstants.h:65
BamTools::Constants::SAM_PG_COMMANDLINE_TAG
const std::string SAM_PG_COMMANDLINE_TAG
Definition SamConstants.h:61
BamTools::Constants::SAM_TAB
const char SAM_TAB
Definition SamConstants.h:24
BamTools::Constants::SAM_SQ_CHECKSUM_TAG
const std::string SAM_SQ_CHECKSUM_TAG
Definition SamConstants.h:38
BamTools::Constants::SAM_RG_SEQTECHNOLOGY_SOLID
const std::string SAM_RG_SEQTECHNOLOGY_SOLID
Definition SamConstants.h:92
BamTools::Constants::SAM_SQ_LENGTH_MIN
const unsigned int SAM_SQ_LENGTH_MIN
Definition SamConstants.h:82
BamTools::Constants::SAM_STAR
const char SAM_STAR
Definition SamConstants.h:23
BamTools::Constants::SAM_RG_ID_TAG
const std::string SAM_RG_ID_TAG
Definition SamConstants.h:48
BamTools::Constants::SAM_SQ_SPECIES_TAG
const std::string SAM_SQ_SPECIES_TAG
Definition SamConstants.h:41
BamTools::Constants::SAM_HD_BEGIN_TOKEN
const std::string SAM_HD_BEGIN_TOKEN
Definition SamConstants.h:30
BamTools::Constants::SAM_EQUAL
const char SAM_EQUAL
Definition SamConstants.h:21
BamTools::Constants::SAM_HD_GROUPORDER_TAG
const std::string SAM_HD_GROUPORDER_TAG
Definition SamConstants.h:33
BamTools::Constants::SAM_SQ_ASSEMBLYID_TAG
const std::string SAM_SQ_ASSEMBLYID_TAG
Definition SamConstants.h:37
BamTools::Constants::SAM_RG_PROGRAM_TAG
const std::string SAM_RG_PROGRAM_TAG
Definition SamConstants.h:54
BamTools
Contains all BamTools classes & methods.
Definition Sort.h:24