BamTools::BamWriter Class Reference

Provides write access for generating BAM files. More...

#include <BamWriter.h>

List of all members.

Public Types
enum	CompressionMode { Compressed = 0, Uncompressed }
	This enum describes the compression behaviors for output BAM files. More...
Public Member Functions
	BamWriter (void)
	constructor
	~BamWriter (void)
	destructor
void	Close (void)
	Closes the current BAM file.
std::string	GetErrorString (void) const
	Returns a human-readable description of the last error that occurred.
bool	IsOpen (void) const
	Returns true if BAM file is open for writing.
bool	Open (const std::string &filename, const std::string &samHeaderText, const RefVector &referenceSequences)
	Opens a BAM file for writing.
bool	Open (const std::string &filename, const SamHeader &samHeader, const RefVector &referenceSequences)
	Opens a BAM file for writing.
bool	SaveAlignment (const BamAlignment &alignment)
	Saves an alignment to the BAM file.
void	SetCompressionMode (const BamWriter::CompressionMode &compressionMode)
	Sets the output compression mode.

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Detailed Description

Provides write access for generating BAM files.

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Member Enumeration Documentation

enum BamTools::BamWriter::CompressionMode

This enum describes the compression behaviors for output BAM files.

Enumerator:

Compressed	Use normal BAM compression.
Uncompressed	Disable BAM compression. Useful in situations where the BAM data is streamed (e.g. piping). It would be wasteful to compress, and then immediately decompress the data.

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Constructor & Destructor Documentation

BamWriter::BamWriter

(

void

)

constructor

BamWriter::~BamWriter

(

void

)

destructor

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Member Function Documentation

void BamWriter::Close

(

void

)

Closes the current BAM file.

See also:

Open()

std::string BamWriter::GetErrorString

(

void

)

const

Returns a human-readable description of the last error that occurred.

This method allows elimination of STDERR pollution. Developers of client code may choose how the messages are displayed to the user, if at all.

Returns:

error description

bool BamWriter::IsOpen

(

void

)

const

Returns true if BAM file is open for writing.

See also:

Open()

bool BamWriter::Open	(	const std::string &	filename,
		const SamHeader &	samHeader,
		const RefVector &	referenceSequences
	)

Opens a BAM file for writing.

This is an overloaded function.

Will overwrite the BAM file if it already exists.

Parameters:

[in]	filename	name of output BAM file
[in]	samHeader	header data, wrapped in SamHeader object
[in]	referenceSequences	list of reference entries

Returns:

true if opened successfully

See also:

Close(), IsOpen(), BamReader::GetHeader(), BamReader::GetReferenceData()

bool BamWriter::Open	(	const std::string &	filename,
		const std::string &	samHeaderText,
		const RefVector &	referenceSequences
	)

Opens a BAM file for writing.

Will overwrite the BAM file if it already exists.

Parameters:

[in]	filename	name of output BAM file
[in]	samHeaderText	header data, as SAM-formatted string
[in]	referenceSequences	list of reference entries

Returns:

true if opened successfully

See also:

Close(), IsOpen(), BamReader::GetHeaderText(), BamReader::GetReferenceData()

bool BamWriter::SaveAlignment

(

const BamAlignment &

alignment

)

Saves an alignment to the BAM file.

Parameters:

[in]

alignment

BamAlignment record to save

See also:

BamReader::GetNextAlignment(), BamReader::GetNextAlignmentCore()

void BamWriter::SetCompressionMode

(

const BamWriter::CompressionMode &

compressionMode

)

Sets the output compression mode.

Default mode is BamWriter::Compressed.

Note:

Changing the compression mode is disabled on open files (i.e. the request will be ignored). Be sure to call this function before opening the BAM file.

        BamWriter writer;
        writer.SetCompressionMode(BamWriter::Uncompressed);
        writer.Open( ... );
        // ...

Parameters:

[in]

compressionMode

desired output compression behavior

See also:

IsOpen(), Open()

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The documentation for this class was generated from the following files:

• BamWriter.h
• BamWriter.cpp