public class SAMTextWriter extends SAMFileWriterImpl
Constructor and Description |
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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 |
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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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void |
writeHeader(java.lang.String textHeader)
Write the header text.
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addAlignment, close, getDefaultMaxRecordsInRam, getFileHeader, getSortOrder, setDefaultMaxRecordsInRam, setHeader, setProgressLogger, setSortOrder
public 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 SAMFileWriterImpl
alignment
- SAMRecord.public void writeHeader(java.lang.String textHeader)
writeHeader
in class SAMFileWriterImpl
textHeader
- String containing the text to write.public void finish()
finish
in class SAMFileWriterImpl
public java.lang.String getFilename()
getFilename
in class SAMFileWriterImpl