BamTools
2.5.2
src
api
SamConstants.h
Go to the documentation of this file.
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
16
namespace
BamTools
{
17
namespace
Constants {
18
19
// basic char constants used in SAM format
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
const
std::string
SAM_CURRENT_VERSION
=
"1.4"
;
28
29
// HD entries
30
const
std::string
SAM_HD_BEGIN_TOKEN
=
"@HD"
;
31
const
std::string
SAM_HD_VERSION_TAG
=
"VN"
;
32
const
std::string
SAM_HD_SORTORDER_TAG
=
"SO"
;
33
const
std::string
SAM_HD_GROUPORDER_TAG
=
"GO"
;
34
35
// SQ entries
36
const
std::string
SAM_SQ_BEGIN_TOKEN
=
"@SQ"
;
37
const
std::string
SAM_SQ_ASSEMBLYID_TAG
=
"AS"
;
38
const
std::string
SAM_SQ_CHECKSUM_TAG
=
"M5"
;
39
const
std::string
SAM_SQ_LENGTH_TAG
=
"LN"
;
40
const
std::string
SAM_SQ_NAME_TAG
=
"SN"
;
41
const
std::string
SAM_SQ_SPECIES_TAG
=
"SP"
;
42
const
std::string
SAM_SQ_URI_TAG
=
"UR"
;
43
44
// RG entries
45
const
std::string
SAM_RG_BEGIN_TOKEN
=
"@RG"
;
46
const
std::string
SAM_RG_DESCRIPTION_TAG
=
"DS"
;
47
const
std::string
SAM_RG_FLOWORDER_TAG
=
"FO"
;
48
const
std::string
SAM_RG_ID_TAG
=
"ID"
;
49
const
std::string
SAM_RG_KEYSEQUENCE_TAG
=
"KS"
;
50
const
std::string
SAM_RG_LIBRARY_TAG
=
"LB"
;
51
const
std::string
SAM_RG_PLATFORMUNIT_TAG
=
"PU"
;
52
const
std::string
SAM_RG_PREDICTEDINSERTSIZE_TAG
=
"PI"
;
53
const
std::string
SAM_RG_PRODUCTIONDATE_TAG
=
"DT"
;
54
const
std::string
SAM_RG_PROGRAM_TAG
=
"PG"
;
55
const
std::string
SAM_RG_SAMPLE_TAG
=
"SM"
;
56
const
std::string
SAM_RG_SEQCENTER_TAG
=
"CN"
;
57
const
std::string
SAM_RG_SEQTECHNOLOGY_TAG
=
"PL"
;
58
59
// PG entries
60
const
std::string
SAM_PG_BEGIN_TOKEN
=
"@PG"
;
61
const
std::string
SAM_PG_COMMANDLINE_TAG
=
"CL"
;
62
const
std::string
SAM_PG_ID_TAG
=
"ID"
;
63
const
std::string
SAM_PG_NAME_TAG
=
"PN"
;
64
const
std::string
SAM_PG_PREVIOUSPROGRAM_TAG
=
"PP"
;
65
const
std::string
SAM_PG_VERSION_TAG
=
"VN"
;
66
67
// CO entries
68
const
std::string
SAM_CO_BEGIN_TOKEN
=
"@CO"
;
69
70
// HD:SO values
71
const
std::string
SAM_HD_SORTORDER_COORDINATE
=
"coordinate"
;
72
const
std::string
SAM_HD_SORTORDER_QUERYNAME
=
"queryname"
;
73
const
std::string
SAM_HD_SORTORDER_UNKNOWN
=
"unknown"
;
74
const
std::string
SAM_HD_SORTORDER_UNSORTED
=
"unsorted"
;
75
76
// HD:GO values
77
const
std::string
SAM_HD_GROUPORDER_NONE
=
"none"
;
78
const
std::string
SAM_HD_GROUPORDER_QUERY
=
"query"
;
79
const
std::string
SAM_HD_GROUPORDER_REFERENCE
=
"reference"
;
80
81
// SQ:LN values
82
const
unsigned
int
SAM_SQ_LENGTH_MIN
= 1;
83
const
unsigned
int
SAM_SQ_LENGTH_MAX
= 536870911;
// 2^29 - 1
84
85
// RG:PL values
86
const
std::string
SAM_RG_SEQTECHNOLOGY_CAPILLARY
=
"CAPILLARY"
;
87
const
std::string
SAM_RG_SEQTECHNOLOGY_HELICOS
=
"HELICOS"
;
88
const
std::string
SAM_RG_SEQTECHNOLOGY_ILLUMINA
=
"ILLUMINA"
;
89
const
std::string
SAM_RG_SEQTECHNOLOGY_IONTORRENT
=
"IONTORRENT"
;
90
const
std::string
SAM_RG_SEQTECHNOLOGY_LS454
=
"LS454"
;
91
const
std::string
SAM_RG_SEQTECHNOLOGY_PACBIO
=
"PACBIO"
;
92
const
std::string
SAM_RG_SEQTECHNOLOGY_SOLID
=
"SOLID"
;
93
94
}
// namespace Constants
95
}
// namespace BamTools
96
97
#endif
// SAM_CONSTANTS_H
api_global.h
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
Generated by
1.9.1