org.seqdoop.hadoop_bam

Class SplittingBAMIndexer

java.lang.Object

org.seqdoop.hadoop_bam.SplittingBAMIndexer

public final class SplittingBAMIndexer
extends Object

An indexing tool and API for BAM files, making them palatable to BAMInputFormat. Writes splitting BAM indices as understood by SplittingBAMIndex. There are two ways of using this class: 1) Building a splitting BAM index from an existing BAM file 2) Building a splitting BAM index while building the BAM file For 1), use the static index(InputStream, OutputStream, long, int) method, which takes the input BAM and output stream to write the index to. For 2), use one of the constructors that takes an output stream, then pass SAMRecord objects via the processAlignment(htsjdk.samtools.SAMRecord) method, and then call finish(long) to complete writing the index.

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_GRANULARITY
static String	OUTPUT_FILE_EXTENSION

Constructor Summary

Constructors

Constructor and Description
SplittingBAMIndexer(int g) Deprecated. use one of the other constructors to create an index while building a BAM file or index(InputStream, OutputStream, long, int) for an existing BAM file.
SplittingBAMIndexer(OutputStream out) Prepare to index a BAM file.
SplittingBAMIndexer(OutputStream out, int granularity) Prepare to index a BAM file.

Method Summary

Modifier and Type	Method and Description
void	finish(long inputSize) Complete the index by writing the input BAM file size to the index, and closing the output stream.
static void	index(InputStream rawIn, OutputStream out, long inputSize, int granularity) Perform indexing on the given BAM file, at the granularity level specified.
static void	main(String[] args)
void	processAlignment(htsjdk.samtools.SAMRecord rec) Process the given record for the index.
static void	run(org.apache.hadoop.conf.Configuration conf) Invoke a new SplittingBAMIndexer object, operating on the supplied Configuration object instead of a supplied argument list
void	writeVirtualOffset(long virtualOffset) Write the given virtual offset to the index.

Methods inherited from class java.lang.Object

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

Field Detail

OUTPUT_FILE_EXTENSION

public static final String OUTPUT_FILE_EXTENSION

See Also:

Constant Field Values

DEFAULT_GRANULARITY

public static final int DEFAULT_GRANULARITY

See Also:

Constant Field Values

Constructor Detail

SplittingBAMIndexer

@Deprecated
public SplittingBAMIndexer(int g)

Deprecated. use one of the other constructors to create an index while building a BAM file or index(InputStream, OutputStream, long, int) for an existing BAM file.

Constructor that allows immediate specification of the granularity level for a new SplittingBAMIndexer.

Parameters:

g - granularity level

SplittingBAMIndexer

public SplittingBAMIndexer(OutputStream out)

Prepare to index a BAM file.

Parameters:

out - the stream to write the index to

SplittingBAMIndexer

public SplittingBAMIndexer(OutputStream out,
                           int granularity)

Prepare to index a BAM file.

Parameters:

out - the stream to write the index to

granularity - write the offset of every n-th alignment to the index

Method Detail

main

public static void main(String[] args)

run

public static void run(org.apache.hadoop.conf.Configuration conf)
                throws IOException

Invoke a new SplittingBAMIndexer object, operating on the supplied Configuration object instead of a supplied argument list

Throws:

IllegalArgumentException - if the "input" property is not in the Configuration

IOException

processAlignment

public void processAlignment(htsjdk.samtools.SAMRecord rec)
                      throws IOException

Process the given record for the index.

Parameters:

rec - the record from the file being indexed

Throws:

IOException

writeVirtualOffset

public void writeVirtualOffset(long virtualOffset)
                        throws IOException

Write the given virtual offset to the index. This method is for internal use only.

Parameters:

virtualOffset - virtual file pointer

Throws:

IOException

finish

public void finish(long inputSize)
            throws IOException

Complete the index by writing the input BAM file size to the index, and closing the output stream.

Parameters:

inputSize - the size of the input BAM file

Throws:

IOException

index

public static void index(InputStream rawIn,
                         OutputStream out,
                         long inputSize,
                         int granularity)
                  throws IOException

Perform indexing on the given BAM file, at the granularity level specified.

Throws:

IOException