org.seqdoop.hadoop_bam

Class BAMSplitGuesser

java.lang.Object

org.seqdoop.hadoop_bam.BAMSplitGuesser

public class BAMSplitGuesser
extends Object

A class for heuristically finding BAM record positions inside an area of a BAM file.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	BaseSplitGuesser.PosSize

Field Summary

Fields

Modifier and Type	Field and Description
protected static int	BGZF_MAGIC
protected static int	BGZF_MAGIC_SUB
protected static int	BGZF_SUB_SIZE
protected ByteBuffer	buf
protected htsjdk.samtools.seekablestream.SeekableStream	in

Constructor Summary

Constructors

Constructor and Description
BAMSplitGuesser(htsjdk.samtools.seekablestream.SeekableStream ss, org.apache.hadoop.conf.Configuration conf) The stream must point to a valid BAM file, because the header is read from it.
BAMSplitGuesser(htsjdk.samtools.seekablestream.SeekableStream ss, InputStream headerStream, org.apache.hadoop.conf.Configuration conf)

Method Summary

Modifier and Type	Method and Description
protected int	getUShort(int idx)
long	guessNextBAMRecordStart(long beg, long end) Finds a virtual BAM record position in the physical position range [beg,end).
protected BaseSplitGuesser.PosSize	guessNextBGZFPos(int p, int end)
static void	main(String[] args)

Methods inherited from class java.lang.Object

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

Field Detail

BGZF_MAGIC

protected static final int BGZF_MAGIC

See Also:

Constant Field Values

BGZF_MAGIC_SUB

protected static final int BGZF_MAGIC_SUB

See Also:

Constant Field Values

BGZF_SUB_SIZE

protected static final int BGZF_SUB_SIZE

See Also:

Constant Field Values

in

protected htsjdk.samtools.seekablestream.SeekableStream in

buf

protected final ByteBuffer buf

Constructor Detail

BAMSplitGuesser

public BAMSplitGuesser(htsjdk.samtools.seekablestream.SeekableStream ss,
                       org.apache.hadoop.conf.Configuration conf)
                throws IOException

The stream must point to a valid BAM file, because the header is read from it.

Throws:

IOException

BAMSplitGuesser

public BAMSplitGuesser(htsjdk.samtools.seekablestream.SeekableStream ss,
                       InputStream headerStream,
                       org.apache.hadoop.conf.Configuration conf)
                throws IOException

Throws:

IOException

Method Detail

guessNextBAMRecordStart

public long guessNextBAMRecordStart(long beg,
                                    long end)
                             throws IOException

Finds a virtual BAM record position in the physical position range [beg,end). Returns end if no BAM record was found.

Throws:

IOException

main

public static void main(String[] args)
                 throws IOException

Throws:

IOException

guessNextBGZFPos

protected BaseSplitGuesser.PosSize guessNextBGZFPos(int p,
                                                    int end)

getUShort

protected int getUShort(int idx)