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.

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
long	guessNextBCFRecordStart(long beg, long end) Finds a (virtual in the case of BGZF) BCF record position in the physical position range [beg,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

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