public class SAMTextWriter extends SAMFileWriterImpl
| Constructor and Description |
|---|
SAMTextWriter(java.io.File file)
Constructs a SAMTextWriter that writes to a File.
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SAMTextWriter(java.io.File file,
SamFlagField samFlagFieldOutput)
Constructs a SAMTextWriter that writes to a File.
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SAMTextWriter(java.io.OutputStream stream)
Constructs a SAMTextWriter that writes to an OutputStream.
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SAMTextWriter(java.io.OutputStream stream,
SamFlagField samFlagFieldOutput)
Constructs a SAMTextWriter that writes to an OutputStream.
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SAMTextWriter(java.io.Writer out)
Constructs a SAMTextWriter that outputs to a Writer.
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SAMTextWriter(java.io.Writer out,
SamFlagField samFlagFieldOutput)
Constructs a SAMTextWriter that outputs to a Writer.
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| Modifier and Type | Method and Description |
|---|---|
void |
finish()
Do any required flushing here.
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java.lang.String |
getFilename()
For producing error messages.
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java.io.Writer |
getWriter()
Returns the Writer used by this instance.
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void |
writeAlignment(SAMRecord alignment)
Write the record.
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protected void |
writeHeader(SAMFileHeader header)
Write the header to disk.
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void |
writeHeader(java.lang.String textHeader)
Write the header text.
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addAlignment, close, getDefaultMaxRecordsInRam, getFileHeader, getMaxRecordsInRam, getSortOrder, getTempDirectory, setDefaultMaxRecordsInRam, setHeader, setMaxRecordsInRam, setProgressLogger, setSortOrder, setTempDirectorypublic SAMTextWriter(java.io.Writer out)
out - Writer.public SAMTextWriter(java.io.File file)
file - Where to write the output.public SAMTextWriter(java.io.OutputStream stream)
stream - Need not be buffered because this class provides buffering.public SAMTextWriter(java.io.Writer out,
SamFlagField samFlagFieldOutput)
out - Writer.public SAMTextWriter(java.io.File file,
SamFlagField samFlagFieldOutput)
file - Where to write the output.public SAMTextWriter(java.io.OutputStream stream,
SamFlagField samFlagFieldOutput)
stream - Need not be buffered because this class provides buffering.public java.io.Writer getWriter()
public void writeAlignment(SAMRecord alignment)
writeAlignment in class SAMFileWriterImplalignment - SAMRecord.public void writeHeader(java.lang.String textHeader)
writeHeader in class SAMFileWriterImpltextHeader - String containing the text to write.protected void writeHeader(SAMFileHeader header)
SAMFileWriterImplIMPORTANT: 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).
writeHeader in class SAMFileWriterImplheader - object to write.public void finish()
finish in class SAMFileWriterImplpublic java.lang.String getFilename()
getFilename in class SAMFileWriterImpl