org.seqdoop.hadoop_bam

Class BCFSplitGuesser

java.lang.Object

org.seqdoop.hadoop_bam.BCFSplitGuesser

public class BCFSplitGuesser
extends Object

A class for heuristically finding BCF record positions inside an area of a BCF file. Handles both compressed and uncompressed BCF.

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
BCFSplitGuesser(htsjdk.samtools.seekablestream.SeekableStream ss) The stream must point to a valid BCF file, because the header is read from it.
BCFSplitGuesser(htsjdk.samtools.seekablestream.SeekableStream ss, InputStream headerStream)

Method Summary

Modifier and Type	Method and Description
protected int	getUShort(int idx)
long	guessNextBCFRecordStart(long beg, long end) Finds a (virtual in the case of BGZF) BCF record position in the physical position range [beg,end).
protected BaseSplitGuesser.PosSize	guessNextBGZFPos(int p, int end)
boolean	isBGZF()
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

BCFSplitGuesser

public BCFSplitGuesser(htsjdk.samtools.seekablestream.SeekableStream ss)
                throws IOException

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

Throws:

IOException

BCFSplitGuesser

public BCFSplitGuesser(htsjdk.samtools.seekablestream.SeekableStream ss,
                       InputStream headerStream)
                throws IOException

Throws:

IOException

Method Detail

isBGZF

public boolean isBGZF()

guessNextBCFRecordStart

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

Finds a (virtual in the case of BGZF) BCF record position in the physical position range [beg,end). Returns end if no BCF 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)