Package htsjdk.samtools
Class SAMTextWriter
- java.lang.Object
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- htsjdk.samtools.SAMFileWriterImpl
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- htsjdk.samtools.SAMTextWriter
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- All Implemented Interfaces:
SAMFileWriter
,Closeable
,AutoCloseable
public class SAMTextWriter extends SAMFileWriterImpl
Writer for text-format SAM files.
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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.
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Method Summary
All Methods Instance Methods Concrete Methods 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, setTempDirectory
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Constructor Detail
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SAMTextWriter
public SAMTextWriter(Writer out)
Constructs a SAMTextWriter that outputs to a Writer.- Parameters:
out
- Writer.
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SAMTextWriter
public SAMTextWriter(File file)
Constructs a SAMTextWriter that writes to a File.- Parameters:
file
- Where to write the output.
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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.
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SAMTextWriter
public SAMTextWriter(Writer out, SamFlagField samFlagFieldOutput)
Constructs a SAMTextWriter that outputs to a Writer.- Parameters:
out
- Writer.
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SAMTextWriter
public SAMTextWriter(File file, SamFlagField samFlagFieldOutput)
Constructs a SAMTextWriter that writes to a File.- Parameters:
file
- Where to write the output.
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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.
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Method Detail
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getWriter
public Writer getWriter()
Returns the Writer used by this instance. Useful for flushing the output.
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writeAlignment
public void writeAlignment(SAMRecord alignment)
Write the record.- Specified by:
writeAlignment
in classSAMFileWriterImpl
- Parameters:
alignment
- SAMRecord.
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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 classSAMFileWriterImpl
- Parameters:
textHeader
- String containing the text to write.
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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 callsSAMFileWriterImpl.writeHeader(String)
.- Overrides:
writeHeader
in classSAMFileWriterImpl
- Parameters:
header
- object to write.
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finish
public void finish()
Do any required flushing here.- Specified by:
finish
in classSAMFileWriterImpl
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getFilename
public String getFilename()
For producing error messages.- Specified by:
getFilename
in classSAMFileWriterImpl
- Returns:
- Output filename, or null if there isn't one.
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