Package htsjdk.samtools

Class SAMTextWriter

java.lang.Object

htsjdk.samtools.SAMFileWriterImpl

htsjdk.samtools.SAMTextWriter

All Implemented Interfaces:

SAMFileWriter, Closeable, AutoCloseable

public class SAMTextWriter
extends SAMFileWriterImpl

Writer for text-format SAM files.

Constructor Summary

Constructors

Constructor	Description
SAMTextWriter(File file)	Constructs a SAMTextWriter that writes to a File.
SAMTextWriter(File file, SamFlagField samFlagFieldOutput)	Constructs a SAMTextWriter that writes to a File.
SAMTextWriter(OutputStream stream)	Constructs a SAMTextWriter that writes to an OutputStream.
SAMTextWriter(OutputStream stream, SamFlagField samFlagFieldOutput)	Constructs a SAMTextWriter that writes to an OutputStream.
SAMTextWriter(Writer out)	Constructs a SAMTextWriter that outputs to a Writer.
SAMTextWriter(Writer out, SamFlagField samFlagFieldOutput)	Constructs a SAMTextWriter that outputs to a Writer.

Method Summary

Modifier and Type	Method	Description
void	finish()	Do any required flushing here.
String	getFilename()	For producing error messages.
Writer	getWriter()	Returns the Writer used by this instance.
void	writeAlignment(SAMRecord alignment)	Write the record.
protected void	writeHeader(SAMFileHeader header)	Write the header to disk.
void	writeHeader(String textHeader)	Write the header text.

Methods inherited from class htsjdk.samtools.SAMFileWriterImpl

addAlignment, close, getDefaultMaxRecordsInRam, getFileHeader, getMaxRecordsInRam, getSortOrder, getTempDirectory, setDefaultMaxRecordsInRam, setHeader, setMaxRecordsInRam, setProgressLogger, setSortOrder, setSortOrderChecking, setTempDirectory

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

SAMTextWriter

public SAMTextWriter(Writer out)

Constructs a SAMTextWriter that outputs to a Writer.

Parameters:

out - Writer.

SAMTextWriter

public SAMTextWriter(File file)

Constructs a SAMTextWriter that writes to a File.

Parameters:

file - Where to write the output.

SAMTextWriter

public SAMTextWriter(OutputStream stream)

Constructs a SAMTextWriter that writes to an OutputStream. The OutputStream is wrapped in an AsciiWriter, which can be retrieved with getWriter().

Parameters:

stream - Need not be buffered because this class provides buffering.

SAMTextWriter

public SAMTextWriter(Writer out,
 SamFlagField samFlagFieldOutput)

Constructs a SAMTextWriter that outputs to a Writer.

Parameters:

out - Writer.

SAMTextWriter

public SAMTextWriter(File file,
 SamFlagField samFlagFieldOutput)

Constructs a SAMTextWriter that writes to a File.

Parameters:

file - Where to write the output.

SAMTextWriter

public SAMTextWriter(OutputStream stream,
 SamFlagField samFlagFieldOutput)

Constructs a SAMTextWriter that writes to an OutputStream. The OutputStream is wrapped in an AsciiWriter, which can be retrieved with getWriter().

Parameters:

stream - Need not be buffered because this class provides buffering.

Method Details

getWriter

public Writer getWriter()

Returns the Writer used by this instance. Useful for flushing the output.

writeAlignment

public void writeAlignment(SAMRecord alignment)

Write the record.

Specified by:

writeAlignment in class SAMFileWriterImpl

Parameters:

alignment - SAMRecord.

writeHeader

public void writeHeader(String textHeader)

Write the header text. This method can also be used to write an arbitrary String, not necessarily the header.

Specified by:

writeHeader in class SAMFileWriterImpl

Parameters:

textHeader - String containing the text to write.

writeHeader

protected void writeHeader(SAMFileHeader header)

Description copied from class: SAMFileWriterImpl

Write the header to disk. Header object is available via getHeader().

IMPORTANT: this method will be abstract once SAMFileWriterImpl.writeHeader(String) is removed.

Note: default implementation uses SAMTextHeaderCodec.encode(java.io.Writer, htsjdk.samtools.SAMFileHeader) and calls SAMFileWriterImpl.writeHeader(String).

Overrides:

writeHeader in class SAMFileWriterImpl

Parameters:

header - object to write.

finish

public void finish()

Do any required flushing here.

Specified by:

finish in class SAMFileWriterImpl

getFilename

public String getFilename()

For producing error messages.

Specified by:

getFilename in class SAMFileWriterImpl

Returns:

Output filename, or null if there isn't one.