htsjdk.samtools

Class SAMFileWriterImpl

java.lang.Object

htsjdk.samtools.SAMFileWriterImpl

All Implemented Interfaces:

SAMFileWriter, java.io.Closeable, java.lang.AutoCloseable

Direct Known Subclasses:

CRAMFileWriter, SAMTextWriter

public abstract class SAMFileWriterImpl
extends java.lang.Object
implements SAMFileWriter

Base class for implementing SAM writer with any underlying format. Mostly this manages accumulation & sorting of SAMRecords when appropriate, and produces the text version of the header, since that seems to be a popular item in both text and binary file formats.

Constructor Summary

Constructors

Constructor and Description
SAMFileWriterImpl()

Method Summary

Methods

Modifier and Type	Method and Description
void	addAlignment(SAMRecord alignment)
void	close() Must be called or else file will likely be defective.
protected abstract void	finish() Do any required flushing here.
static int	getDefaultMaxRecordsInRam() When writing records that are not presorted, this number determines the number of records stored in RAM before spilling to disk.
SAMFileHeader	getFileHeader()
protected abstract java.lang.String	getFilename() For producing error messages.
protected SAMFileHeader.SortOrder	getSortOrder() Must be called after calling setHeader().
static void	setDefaultMaxRecordsInRam(int maxRecordsInRam) When writing records that are not presorted, specify the number of records stored in RAM before spilling to disk.
void	setHeader(SAMFileHeader header) Must be called before addAlignment.
void	setProgressLogger(ProgressLoggerInterface progress) Sets the progress logger used by this implementation.
void	setSortOrder(SAMFileHeader.SortOrder sortOrder, boolean presorted) Must be called before calling setHeader().
protected abstract void	writeAlignment(SAMRecord alignment) Writes the record to disk.
protected abstract void	writeHeader(java.lang.String textHeader) Write the header to disk.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SAMFileWriterImpl

public SAMFileWriterImpl()

Method Detail

setDefaultMaxRecordsInRam

public static void setDefaultMaxRecordsInRam(int maxRecordsInRam)

When writing records that are not presorted, specify the number of records stored in RAM before spilling to disk. This method sets the default value for all SamFileWriterImpl instances. Must be called before the constructor is called.

Parameters:

maxRecordsInRam -

getDefaultMaxRecordsInRam

public static int getDefaultMaxRecordsInRam()

When writing records that are not presorted, this number determines the number of records stored in RAM before spilling to disk.

Returns:

DEAFULT_MAX_RECORDS_IN_RAM

setProgressLogger

public void setProgressLogger(ProgressLoggerInterface progress)

Sets the progress logger used by this implementation. Setting this lets this writer emit log messages as SAM records in a SortingCollection are being written to disk.

Specified by:

setProgressLogger in interface SAMFileWriter

setSortOrder

public void setSortOrder(SAMFileHeader.SortOrder sortOrder,
                boolean presorted)

Must be called before calling setHeader(). SortOrder value in the header passed to setHeader() is ignored. If setSortOrder is not called, default is SortOrder.unsorted.

getSortOrder

protected SAMFileHeader.SortOrder getSortOrder()

Must be called after calling setHeader().

setHeader

public void setHeader(SAMFileHeader header)

Must be called before addAlignment.

getFileHeader

public SAMFileHeader getFileHeader()

Specified by:

getFileHeader in interface SAMFileWriter

addAlignment

public void addAlignment(SAMRecord alignment)

Specified by:

addAlignment in interface SAMFileWriter

close

public final void close()

Must be called or else file will likely be defective.

Specified by:

close in interface SAMFileWriter

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

writeAlignment

protected abstract void writeAlignment(SAMRecord alignment)

Writes the record to disk. Sort order has been taken care of by the time this method is called.

Parameters:

alignment -

writeHeader

protected abstract void writeHeader(java.lang.String textHeader)

Write the header to disk. Header object is available via getHeader().

Parameters:

textHeader - for convenience if the implementation needs it.

finish

protected abstract void finish()

Do any required flushing here.

getFilename

protected abstract java.lang.String getFilename()

For producing error messages.

Returns:

Output filename, or null if there isn't one.