public class SAMTextWriter extends SAMFileWriterImpl
| Constructor and 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.
|
| Modifier and Type | Method and 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.
|
addAlignment, close, getDefaultMaxRecordsInRam, getFileHeader, getSortOrder, setDefaultMaxRecordsInRam, setHeader, setProgressLogger, setSortOrderpublic 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 SAMFileWriterImplalignment - SAMRecord.public void writeHeader(String textHeader)
writeHeader in class SAMFileWriterImpltextHeader - String containing the text to write.public void finish()
finish in class SAMFileWriterImplpublic String getFilename()
getFilename in class SAMFileWriterImpl