org.seqdoop.hadoop_bam

Class FileVirtualSplit

java.lang.Object

org.apache.hadoop.mapreduce.InputSplit

org.seqdoop.hadoop_bam.FileVirtualSplit

All Implemented Interfaces:

org.apache.hadoop.io.Writable

public class FileVirtualSplit
extends org.apache.hadoop.mapreduce.InputSplit
implements org.apache.hadoop.io.Writable

Like a FileSplit, but uses BGZF virtual offsets to fit with BlockCompressedInputStream.

Constructor Summary

Constructors

Constructor and Description
FileVirtualSplit()
FileVirtualSplit(org.apache.hadoop.fs.Path f, long vs, long ve, String[] locs)
FileVirtualSplit(org.apache.hadoop.fs.Path f, long vs, long ve, String[] locs, long[] intervalFilePointers)

Method Summary

Modifier and Type	Method and Description
long	getEndVirtualOffset() Exclusive.
long[]	getIntervalFilePointers()
long	getLength() Inexact due to the nature of virtual offsets.
String[]	getLocations()
org.apache.hadoop.fs.Path	getPath()
long	getStartVirtualOffset() Inclusive.
void	readFields(DataInput in)
void	setEndVirtualOffset(long vo)
void	setStartVirtualOffset(long vo)
String	toString()
void	write(DataOutput out)

Methods inherited from class java.lang.Object

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

Constructor Detail

FileVirtualSplit

public FileVirtualSplit()

FileVirtualSplit

public FileVirtualSplit(org.apache.hadoop.fs.Path f,
                        long vs,
                        long ve,
                        String[] locs)

FileVirtualSplit

public FileVirtualSplit(org.apache.hadoop.fs.Path f,
                        long vs,
                        long ve,
                        String[] locs,
                        long[] intervalFilePointers)

Method Detail

getLocations

public String[] getLocations()

Specified by:

getLocations in class org.apache.hadoop.mapreduce.InputSplit

getLength

public long getLength()

Inexact due to the nature of virtual offsets. We can't know how many blocks there are in between two file offsets, nor how large those blocks are. So this uses only the difference between the file offsets—unless that difference is zero, in which case the split is wholly contained in one block and thus we can give an exact result.

Specified by:

getLength in class org.apache.hadoop.mapreduce.InputSplit

getPath

public org.apache.hadoop.fs.Path getPath()

getStartVirtualOffset

public long getStartVirtualOffset()

Inclusive.

getEndVirtualOffset

public long getEndVirtualOffset()

Exclusive.

setStartVirtualOffset

public void setStartVirtualOffset(long vo)

setEndVirtualOffset

public void setEndVirtualOffset(long vo)

getIntervalFilePointers

public long[] getIntervalFilePointers()

Returns:

pairs of virtual file pointers for all intervals that should be used for filtering the split, or null if there are none. These correspond to BAMFileSpan chunk start/stop pointers in htsjdk.

write

public void write(DataOutput out)
           throws IOException

Specified by:

write in interface org.apache.hadoop.io.Writable

Throws:

IOException

readFields

public void readFields(DataInput in)
                throws IOException

Specified by:

readFields in interface org.apache.hadoop.io.Writable

Throws:

IOException

toString

public String toString()

Overrides:

toString in class Object