BamTools 2.5.2
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SamConstants.h
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1// ***************************************************************************
2// SamConstants.h (c) 2010 Derek Barnett
3// Marth Lab, Department of Biology, Boston College
4// ---------------------------------------------------------------------------
5// Last modified: 27 March 2012 (DB)
6// ---------------------------------------------------------------------------
7// Provides constants for SAM header
8// ***************************************************************************
9
10#ifndef SAM_CONSTANTS_H
11#define SAM_CONSTANTS_H
12
13#include <string>
14#include "api/api_global.h"
15
16namespace BamTools {
17namespace Constants {
18
19// basic char constants used in SAM format
20const char SAM_COLON = ':';
21const char SAM_EQUAL = '=';
22const char SAM_PERIOD = '.';
23const char SAM_STAR = '*';
24const char SAM_TAB = '\t';
25const std::string SAM_DIGITS = "0123456789";
26
27const std::string SAM_CURRENT_VERSION = "1.4";
28
29// HD entries
30const std::string SAM_HD_BEGIN_TOKEN = "@HD";
31const std::string SAM_HD_VERSION_TAG = "VN";
32const std::string SAM_HD_SORTORDER_TAG = "SO";
33const std::string SAM_HD_GROUPORDER_TAG = "GO";
34
35// SQ entries
36const std::string SAM_SQ_BEGIN_TOKEN = "@SQ";
37const std::string SAM_SQ_ASSEMBLYID_TAG = "AS";
38const std::string SAM_SQ_CHECKSUM_TAG = "M5";
39const std::string SAM_SQ_LENGTH_TAG = "LN";
40const std::string SAM_SQ_NAME_TAG = "SN";
41const std::string SAM_SQ_SPECIES_TAG = "SP";
42const std::string SAM_SQ_URI_TAG = "UR";
43
44// RG entries
45const std::string SAM_RG_BEGIN_TOKEN = "@RG";
46const std::string SAM_RG_DESCRIPTION_TAG = "DS";
47const std::string SAM_RG_FLOWORDER_TAG = "FO";
48const std::string SAM_RG_ID_TAG = "ID";
49const std::string SAM_RG_KEYSEQUENCE_TAG = "KS";
50const std::string SAM_RG_LIBRARY_TAG = "LB";
51const std::string SAM_RG_PLATFORMUNIT_TAG = "PU";
52const std::string SAM_RG_PREDICTEDINSERTSIZE_TAG = "PI";
53const std::string SAM_RG_PRODUCTIONDATE_TAG = "DT";
54const std::string SAM_RG_PROGRAM_TAG = "PG";
55const std::string SAM_RG_SAMPLE_TAG = "SM";
56const std::string SAM_RG_SEQCENTER_TAG = "CN";
57const std::string SAM_RG_SEQTECHNOLOGY_TAG = "PL";
58
59// PG entries
60const std::string SAM_PG_BEGIN_TOKEN = "@PG";
61const std::string SAM_PG_COMMANDLINE_TAG = "CL";
62const std::string SAM_PG_ID_TAG = "ID";
63const std::string SAM_PG_NAME_TAG = "PN";
64const std::string SAM_PG_PREVIOUSPROGRAM_TAG = "PP";
65const std::string SAM_PG_VERSION_TAG = "VN";
66
67// CO entries
68const std::string SAM_CO_BEGIN_TOKEN = "@CO";
69
70// HD:SO values
71const std::string SAM_HD_SORTORDER_COORDINATE = "coordinate";
72const std::string SAM_HD_SORTORDER_QUERYNAME = "queryname";
73const std::string SAM_HD_SORTORDER_UNKNOWN = "unknown";
74const std::string SAM_HD_SORTORDER_UNSORTED = "unsorted";
75
76// HD:GO values
77const std::string SAM_HD_GROUPORDER_NONE = "none";
78const std::string SAM_HD_GROUPORDER_QUERY = "query";
79const std::string SAM_HD_GROUPORDER_REFERENCE = "reference";
80
81// SQ:LN values
82const unsigned int SAM_SQ_LENGTH_MIN = 1;
83const unsigned int SAM_SQ_LENGTH_MAX = 536870911; // 2^29 - 1
84
85// RG:PL values
86const std::string SAM_RG_SEQTECHNOLOGY_CAPILLARY = "CAPILLARY";
87const std::string SAM_RG_SEQTECHNOLOGY_HELICOS = "HELICOS";
88const std::string SAM_RG_SEQTECHNOLOGY_ILLUMINA = "ILLUMINA";
89const std::string SAM_RG_SEQTECHNOLOGY_IONTORRENT = "IONTORRENT";
90const std::string SAM_RG_SEQTECHNOLOGY_LS454 = "LS454";
91const std::string SAM_RG_SEQTECHNOLOGY_PACBIO = "PACBIO";
92const std::string SAM_RG_SEQTECHNOLOGY_SOLID = "SOLID";
93
94} // namespace Constants
95} // namespace BamTools
96
97#endif // SAM_CONSTANTS_H
const char SAM_PERIOD
Definition SamConstants.h:22
const std::string SAM_HD_VERSION_TAG
Definition SamConstants.h:31
const std::string SAM_CURRENT_VERSION
Definition SamConstants.h:27
const std::string SAM_HD_SORTORDER_QUERYNAME
Definition SamConstants.h:72
const std::string SAM_RG_SAMPLE_TAG
Definition SamConstants.h:55
const std::string SAM_PG_BEGIN_TOKEN
Definition SamConstants.h:60
const std::string SAM_HD_SORTORDER_TAG
Definition SamConstants.h:32
const std::string SAM_SQ_BEGIN_TOKEN
Definition SamConstants.h:36
const std::string SAM_PG_PREVIOUSPROGRAM_TAG
Definition SamConstants.h:64
const std::string SAM_HD_SORTORDER_UNSORTED
Definition SamConstants.h:74
const std::string SAM_SQ_LENGTH_TAG
Definition SamConstants.h:39
const std::string SAM_HD_GROUPORDER_NONE
Definition SamConstants.h:77
const std::string SAM_RG_PRODUCTIONDATE_TAG
Definition SamConstants.h:53
const std::string SAM_RG_SEQTECHNOLOGY_ILLUMINA
Definition SamConstants.h:88
const std::string SAM_RG_BEGIN_TOKEN
Definition SamConstants.h:45
const char SAM_COLON
Definition SamConstants.h:20
const std::string SAM_SQ_NAME_TAG
Definition SamConstants.h:40
const std::string SAM_PG_ID_TAG
Definition SamConstants.h:62
const std::string SAM_RG_KEYSEQUENCE_TAG
Definition SamConstants.h:49
const std::string SAM_HD_SORTORDER_UNKNOWN
Definition SamConstants.h:73
const std::string SAM_RG_LIBRARY_TAG
Definition SamConstants.h:50
const std::string SAM_HD_GROUPORDER_REFERENCE
Definition SamConstants.h:79
const std::string SAM_HD_SORTORDER_COORDINATE
Definition SamConstants.h:71
const std::string SAM_RG_SEQTECHNOLOGY_HELICOS
Definition SamConstants.h:87
const unsigned int SAM_SQ_LENGTH_MAX
Definition SamConstants.h:83
const std::string SAM_PG_NAME_TAG
Definition SamConstants.h:63
const std::string SAM_RG_DESCRIPTION_TAG
Definition SamConstants.h:46
const std::string SAM_RG_PREDICTEDINSERTSIZE_TAG
Definition SamConstants.h:52
const std::string SAM_RG_SEQTECHNOLOGY_TAG
Definition SamConstants.h:57
const std::string SAM_RG_PLATFORMUNIT_TAG
Definition SamConstants.h:51
const std::string SAM_DIGITS
Definition SamConstants.h:25
const std::string SAM_RG_SEQTECHNOLOGY_CAPILLARY
Definition SamConstants.h:86
const std::string SAM_HD_GROUPORDER_QUERY
Definition SamConstants.h:78
const std::string SAM_CO_BEGIN_TOKEN
Definition SamConstants.h:68
const std::string SAM_RG_SEQTECHNOLOGY_IONTORRENT
Definition SamConstants.h:89
const std::string SAM_RG_SEQTECHNOLOGY_PACBIO
Definition SamConstants.h:91
const std::string SAM_RG_SEQCENTER_TAG
Definition SamConstants.h:56
const std::string SAM_SQ_URI_TAG
Definition SamConstants.h:42
const std::string SAM_RG_SEQTECHNOLOGY_LS454
Definition SamConstants.h:90
const std::string SAM_RG_FLOWORDER_TAG
Definition SamConstants.h:47
const std::string SAM_PG_VERSION_TAG
Definition SamConstants.h:65
const std::string SAM_PG_COMMANDLINE_TAG
Definition SamConstants.h:61
const char SAM_TAB
Definition SamConstants.h:24
const std::string SAM_SQ_CHECKSUM_TAG
Definition SamConstants.h:38
const std::string SAM_RG_SEQTECHNOLOGY_SOLID
Definition SamConstants.h:92
const unsigned int SAM_SQ_LENGTH_MIN
Definition SamConstants.h:82
const char SAM_STAR
Definition SamConstants.h:23
const std::string SAM_RG_ID_TAG
Definition SamConstants.h:48
const std::string SAM_SQ_SPECIES_TAG
Definition SamConstants.h:41
const std::string SAM_HD_BEGIN_TOKEN
Definition SamConstants.h:30
const char SAM_EQUAL
Definition SamConstants.h:21
const std::string SAM_HD_GROUPORDER_TAG
Definition SamConstants.h:33
const std::string SAM_SQ_ASSEMBLYID_TAG
Definition SamConstants.h:37
const std::string SAM_RG_PROGRAM_TAG
Definition SamConstants.h:54
Contains all BamTools classes & methods.
Definition Sort.h:24