Package htsjdk.samtools

Interface SAMFileWriter

All Superinterfaces:

AutoCloseable, Closeable

All Known Implementing Classes:

BAMFileWriter, CRAMFileWriter, SAMFileWriterImpl, SAMTextWriter

public interface SAMFileWriter
extends Closeable

Interface for SAMText and BAM file writers. Clients need not care which they write to, once the object is constructed.

Method Summary

Modifier and Type	Method	Description
void	addAlignment(SAMRecord alignment)
void	close()	Must be called to flush or file will likely be defective.
SAMFileHeader	getFileHeader()
void	setProgressLogger(ProgressLoggerInterface progress)	Sets a ProgressLogger on this writer.
default void	setSortOrderChecking(boolean check)	If true writers that are writing pre-sorted records should check the order during writing.

Method Details

addAlignment

void addAlignment(SAMRecord alignment)

getFileHeader

SAMFileHeader getFileHeader()

setProgressLogger

void setProgressLogger(ProgressLoggerInterface progress)

Sets a ProgressLogger on this writer. This is useful when pulling, for instance, from a SortingCollection.

setSortOrderChecking

default void setSortOrderChecking(boolean check)

If true writers that are writing pre-sorted records should check the order during writing.

close

void close()

Must be called to flush or file will likely be defective.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable