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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bamgraph_8hpp_source.html below:

NCBI C++ ToolKit: include/sra/readers/bam/bamgraph.hpp Source File

1 #ifndef SRA__READER__BAM__BAMGRAPH__HPP 2 #define SRA__READER__BAM__BAMGRAPH__HPP 79 const string

& GetRefLabel(

void

)

const

;

80 void

SetRefLabel(

const string

& ref_label);

83 const CSeq_id

& GetRefId(

void

)

const

;

84 void

SetRefId(

const CSeq_id

& ref_id);

87 const string

& GetGraphTitle(

void

)

const

;

88 void

SetGraphTitle(

const string

& title);

91 const string

& GetAnnotName(

void

)

const

;

92 void

SetAnnotName(

const string

& name);

98 int

GetMinMapQuality(

void

)

const

;

99 void

SetMinMapQuality(

int

qual);

104

eGraphType_logarithmic

106

EGraphType GetGraphType(

void

)

const

;

107 void

SetGraphType(EGraphType

type

);

114

EGraphValueType GetGraphValueType(

void

)

const

;

115 void

SetGraphValueType(EGraphValueType

type

);

119

kGraphBinSizeFromBAI = 1<<14,

120

kGraphBinSizeFromIndex = 0,

121

kDefaultGraphBinSize = 1000,

125

kEstimatedGraphBinSize

NCBI_STD_DEPRECATED

(

"Use either kGraphBinSizeFromIndex or kGraphBinSizeFromBAI"

) = 1<<14

127 TSeqPos

GetGraphBinSize(

void

)

const

;

128 void

SetGraphBinSize(

TSeqPos

bin_size);

131 double

GetOutlierMax(

void

)

const

;

132 void

SetOutlierMax(

double

x);

133 bool

GetOutlierDetails(

void

)

const

;

134 void

SetOutlierDetails(

bool

details =

true

);

137 bool

GetRawAccess(

void

)

const

;

138 void

SetRawAccess(

bool

raw_access =

true

);

142 bool

GetEstimated(

void

)

const

;

143 void

SetEstimated(

bool

estimated =

true

);

146

vector<Uint8> CollectCoverage(

CBamMgr

& mgr,

147 const string

& bam_file,

148 const string

& bam_index);

149

vector<Uint8> CollectCoverage(

CBamDb

& db);

150

vector<Uint8> CollectCoverage(

CBamRawDb

& db);

151

vector<Uint8> CollectEstimatedCoverage(

const CBamHeader

& header,

153

vector<Uint8> CollectEstimatedCoverage(

CBamRawDb

& db);

154

vector<Uint8> CollectEstimatedCoverage(

CBamDb

& db);

155

vector<Uint8> CollectEstimatedCoverage(

const string

& bam_file,

156 const string

& bam_index);

159

vector<Uint8> CollectRawAccessCoverage(

CBamRawDb

& db);

160

vector<Uint8> CollectRawAccessCoverage(

CBamDb

& db);

161

vector<Uint8> CollectRawAccessCoverage(

const string

& bam_file,

162 const string

& bam_index);

166 const string

& bam_file,

167 const string

& bam_index);

170 const string

& bam_file);

172 const string

& bam_file);

174 const string

& bam_file);

176 const string

& bam_file);

179 const string

& bam_file,

180 const string

& bam_index);

183 const string

& bam_file);

185 const string

& bam_file);

188 const string

& bam_file);

const string & GetRefLabel(void) const

Label of the reference sequence in the BAM file.

EGraphValueType m_GraphValueType

vector< Uint8 > CollectRawAccessCoverage(const CBamHeader &header, const CBamIndex &bam_index)

bool GetEstimated(void) const

make estimated graph using BAM index only the bin size will be derived from index

bool GetOutlierDetails(void) const

const string & GetAnnotName(void) const

Annot name of generated Seq-graph.

bool GetRawAccess(void) const

try to use raw BAM file access for efficiency

CRef< CSeq_inst > m_Seq_inst

const string & GetGraphTitle(void) const

Title of generated Seq-graph.

EGraphType

Type of graph coverage axis - linear or logarithmic.

const CSeq_id & GetRefId(void) const

Seq-id for the reference sequence in generated entry.

EGraphType GetGraphType(void) const

EGraphValueType GetGraphValueType(void) const

EGraphValueType

Type of graph values - byte (0-255) or int.

CRange< TSeqPos > m_TotalRange

TSeqPos GetGraphBinSize(void) const

Include a standard set of the NCBI C++ Toolkit most basic headers.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NCBI_STD_DEPRECATED(message)

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_BAMREAD_EXPORT

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