SAMFileWriter
, Closeable
, AutoCloseable
public class SAMTextWriter extends SAMFileWriterImpl
Constructor | Description |
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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.
|
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.
|
void |
writeHeader(String textHeader) |
Write the header text.
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
addAlignment, close, getDefaultMaxRecordsInRam, getFileHeader, getSortOrder, setDefaultMaxRecordsInRam, setHeader, setProgressLogger, setSortOrder
public SAMTextWriter(Writer out)
out
- Writer.public SAMTextWriter(File file)
file
- Where to write the output.public SAMTextWriter(OutputStream stream)
stream
- Need not be buffered because this class provides buffering.public SAMTextWriter(Writer out, SamFlagField samFlagFieldOutput)
out
- Writer.public SAMTextWriter(File file, SamFlagField samFlagFieldOutput)
file
- Where to write the output.public SAMTextWriter(OutputStream stream, SamFlagField samFlagFieldOutput)
stream
- Need not be buffered because this class provides buffering.public Writer getWriter()
public void writeAlignment(SAMRecord alignment)
writeAlignment
in class SAMFileWriterImpl
alignment
- SAMRecord.public void writeHeader(String textHeader)
writeHeader
in class SAMFileWriterImpl
textHeader
- String containing the text to write.public void finish()
finish
in class SAMFileWriterImpl
public String getFilename()
getFilename
in class SAMFileWriterImpl