BamTools 2.5.2
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Namespaces | Variables
SamConstants.h File Reference
#include <string>
#include "api/api_global.h"

Go to the source code of this file.

Namespaces

namespace  BamTools
 Contains all BamTools classes & methods.
 
namespace  BamTools::Constants
 Provides basic constants for handling BAM files.
 

Variables

const char BamTools::Constants::SAM_COLON = ':'
 
const char BamTools::Constants::SAM_EQUAL = '='
 
const char BamTools::Constants::SAM_PERIOD = '.'
 
const char BamTools::Constants::SAM_STAR = '*'
 
const char BamTools::Constants::SAM_TAB = '\t'
 
const std::string BamTools::Constants::SAM_DIGITS = "0123456789"
 
const std::string BamTools::Constants::SAM_CURRENT_VERSION = "1.4"
 
const std::string BamTools::Constants::SAM_HD_BEGIN_TOKEN = "@HD"
 
const std::string BamTools::Constants::SAM_HD_VERSION_TAG = "VN"
 
const std::string BamTools::Constants::SAM_HD_SORTORDER_TAG = "SO"
 
const std::string BamTools::Constants::SAM_HD_GROUPORDER_TAG = "GO"
 
const std::string BamTools::Constants::SAM_SQ_BEGIN_TOKEN = "@SQ"
 
const std::string BamTools::Constants::SAM_SQ_ASSEMBLYID_TAG = "AS"
 
const std::string BamTools::Constants::SAM_SQ_CHECKSUM_TAG = "M5"
 
const std::string BamTools::Constants::SAM_SQ_LENGTH_TAG = "LN"
 
const std::string BamTools::Constants::SAM_SQ_NAME_TAG = "SN"
 
const std::string BamTools::Constants::SAM_SQ_SPECIES_TAG = "SP"
 
const std::string BamTools::Constants::SAM_SQ_URI_TAG = "UR"
 
const std::string BamTools::Constants::SAM_RG_BEGIN_TOKEN = "@RG"
 
const std::string BamTools::Constants::SAM_RG_DESCRIPTION_TAG = "DS"
 
const std::string BamTools::Constants::SAM_RG_FLOWORDER_TAG = "FO"
 
const std::string BamTools::Constants::SAM_RG_ID_TAG = "ID"
 
const std::string BamTools::Constants::SAM_RG_KEYSEQUENCE_TAG = "KS"
 
const std::string BamTools::Constants::SAM_RG_LIBRARY_TAG = "LB"
 
const std::string BamTools::Constants::SAM_RG_PLATFORMUNIT_TAG = "PU"
 
const std::string BamTools::Constants::SAM_RG_PREDICTEDINSERTSIZE_TAG = "PI"
 
const std::string BamTools::Constants::SAM_RG_PRODUCTIONDATE_TAG = "DT"
 
const std::string BamTools::Constants::SAM_RG_PROGRAM_TAG = "PG"
 
const std::string BamTools::Constants::SAM_RG_SAMPLE_TAG = "SM"
 
const std::string BamTools::Constants::SAM_RG_SEQCENTER_TAG = "CN"
 
const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_TAG = "PL"
 
const std::string BamTools::Constants::SAM_PG_BEGIN_TOKEN = "@PG"
 
const std::string BamTools::Constants::SAM_PG_COMMANDLINE_TAG = "CL"
 
const std::string BamTools::Constants::SAM_PG_ID_TAG = "ID"
 
const std::string BamTools::Constants::SAM_PG_NAME_TAG = "PN"
 
const std::string BamTools::Constants::SAM_PG_PREVIOUSPROGRAM_TAG = "PP"
 
const std::string BamTools::Constants::SAM_PG_VERSION_TAG = "VN"
 
const std::string BamTools::Constants::SAM_CO_BEGIN_TOKEN = "@CO"
 
const std::string BamTools::Constants::SAM_HD_SORTORDER_COORDINATE = "coordinate"
 
const std::string BamTools::Constants::SAM_HD_SORTORDER_QUERYNAME = "queryname"
 
const std::string BamTools::Constants::SAM_HD_SORTORDER_UNKNOWN = "unknown"
 
const std::string BamTools::Constants::SAM_HD_SORTORDER_UNSORTED = "unsorted"
 
const std::string BamTools::Constants::SAM_HD_GROUPORDER_NONE = "none"
 
const std::string BamTools::Constants::SAM_HD_GROUPORDER_QUERY = "query"
 
const std::string BamTools::Constants::SAM_HD_GROUPORDER_REFERENCE = "reference"
 
const unsigned int BamTools::Constants::SAM_SQ_LENGTH_MIN = 1
 
const unsigned int BamTools::Constants::SAM_SQ_LENGTH_MAX = 536870911
 
const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_CAPILLARY = "CAPILLARY"
 
const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_HELICOS = "HELICOS"
 
const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_ILLUMINA = "ILLUMINA"
 
const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_IONTORRENT = "IONTORRENT"
 
const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_LS454 = "LS454"
 
const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_PACBIO = "PACBIO"
 
const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_SOLID = "SOLID"