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.

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
long	guessNextBAMRecordStart(long beg, long end) Finds a virtual BAM record position in the physical position range [beg,end).
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

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