org.seqdoop.hadoop_bam

Class BAMRecordReader

java.lang.Object

org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.LongWritable,SAMRecordWritable>

org.seqdoop.hadoop_bam.BAMRecordReader

All Implemented Interfaces:

Closeable, AutoCloseable

public class BAMRecordReader
extends org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.LongWritable,SAMRecordWritable>

The key is the bitwise OR of the reference sequence ID in the upper 32 bits and the 0-based leftmost coordinate in the lower.

Constructor Summary

Constructors

Constructor and Description
BAMRecordReader()

Method Summary

Modifier and Type	Method and Description
void	close()
org.apache.hadoop.io.LongWritable	getCurrentKey()
SAMRecordWritable	getCurrentValue()
static long	getKey(int refIdx, int alignmentStart)
static long	getKey(htsjdk.samtools.SAMRecord rec) Note: this is the only getKey function that handles unmapped reads specially!
static long	getKey0(int refIdx, int alignmentStart0)
float	getProgress() Unless the end has been reached, this only takes file position into account, not the position within the block.
void	initialize(org.apache.hadoop.mapreduce.InputSplit spl, org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
boolean	nextKeyValue()

Methods inherited from class java.lang.Object

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

Constructor Detail

BAMRecordReader

public BAMRecordReader()

Method Detail

getKey

public static long getKey(htsjdk.samtools.SAMRecord rec)

Note: this is the only getKey function that handles unmapped reads specially!

getKey

public static long getKey(int refIdx,
                          int alignmentStart)

Parameters:

alignmentStart - 1-based leftmost coordinate.

getKey0

public static long getKey0(int refIdx,
                           int alignmentStart0)

Parameters:

alignmentStart0 - 0-based leftmost coordinate.

initialize

public void initialize(org.apache.hadoop.mapreduce.InputSplit spl,
                       org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
                throws IOException

Specified by:

initialize in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.LongWritable,SAMRecordWritable>

Throws:

IOException

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Specified by:

close in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.LongWritable,SAMRecordWritable>

Throws:

IOException

getProgress

public float getProgress()

Unless the end has been reached, this only takes file position into account, not the position within the block.

Specified by:

getProgress in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.LongWritable,SAMRecordWritable>

getCurrentKey

public org.apache.hadoop.io.LongWritable getCurrentKey()

Specified by:

getCurrentKey in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.LongWritable,SAMRecordWritable>

getCurrentValue

public SAMRecordWritable getCurrentValue()

Specified by:

getCurrentValue in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.LongWritable,SAMRecordWritable>

nextKeyValue

public boolean nextKeyValue()

Specified by:

nextKeyValue in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.LongWritable,SAMRecordWritable>