SAMTextWriter (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.samtools.SAMFileWriterImpl
- - htsjdk.samtools.SAMTextWriter

All Implemented Interfaces:

SAMFileWriter, Closeable, AutoCloseable
```
public class SAMTextWriter
extends SAMFileWriterImpl
```
Writer for text-format SAM files.

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.

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.
`void`	`writeHeader(String textHeader)`	Write the header text.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from class htsjdk.samtools.SAMFileWriterImpl
addAlignment, close, getDefaultMaxRecordsInRam, getFileHeader, getSortOrder, setDefaultMaxRecordsInRam, setHeader, setProgressLogger, setSortOrder

- Constructor Detail
  - SAMTextWriter
```
public SAMTextWriter(Writer out)
```
    Constructs a SAMTextWriter that outputs to a Writer.
    
    Parameters:
    
    out - Writer.
  - SAMTextWriter
```
public SAMTextWriter(File file)
```
    Constructs a SAMTextWriter that writes to a File.
    
    Parameters:
    
    file - Where to write the output.
  - 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.
  - SAMTextWriter
```
public SAMTextWriter(Writer out,
                     SamFlagField samFlagFieldOutput)
```
    Constructs a SAMTextWriter that outputs to a Writer.
    
    Parameters:
    
    out - Writer.
  - SAMTextWriter
```
public SAMTextWriter(File file,
                     SamFlagField samFlagFieldOutput)
```
    Constructs a SAMTextWriter that writes to a File.
    
    Parameters:
    
    file - Where to write the output.
  - 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.
- Method Detail
  - getWriter
```
public Writer getWriter()
```
    Returns the Writer used by this instance. Useful for flushing the output.
  - writeAlignment
```
public void writeAlignment(SAMRecord alignment)
```
    Write the record.
    
    Specified by:
    
    writeAlignment in class SAMFileWriterImpl
    
    Parameters:
    
    alignment - SAMRecord.
  - 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 class SAMFileWriterImpl
    
    Parameters:
    
    textHeader - String containing the text to write.
  - finish
```
public void finish()
```
    Do any required flushing here.
    
    Specified by:
    
    finish in class SAMFileWriterImpl
  - getFilename
```
public String getFilename()
```
    For producing error messages.
    
    Specified by:
    
    getFilename in class SAMFileWriterImpl
    
    Returns:
    
    Output filename, or null if there isn't one.

Class SAMTextWriter

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from class htsjdk.samtools.SAMFileWriterImpl

Constructor Detail

SAMTextWriter

SAMTextWriter

SAMTextWriter

SAMTextWriter

SAMTextWriter

SAMTextWriter

Method Detail

getWriter

writeAlignment

writeHeader

finish

getFilename