org.seqdoop.hadoop_bam.util

Class BGZFSplitFileInputFormat<K,V>

java.lang.Object

org.apache.hadoop.mapreduce.InputFormat<K,V>

org.apache.hadoop.mapreduce.lib.input.FileInputFormat<K,V>

org.seqdoop.hadoop_bam.util.BGZFSplitFileInputFormat<K,V>

public abstract class BGZFSplitFileInputFormat<K,V>
extends org.apache.hadoop.mapreduce.lib.input.FileInputFormat<K,V>

An InputFormat for BGZF-compressed files.

A BGZFBlockIndex for each Path used is required, or an IOException is thrown out of getSplits(org.apache.hadoop.mapreduce.JobContext).

Nested Class Summary

Nested classes/interfaces inherited from class org.apache.hadoop.mapreduce.lib.input.FileInputFormat

org.apache.hadoop.mapreduce.lib.input.FileInputFormat.Counter

Field Summary

Fields inherited from class org.apache.hadoop.mapreduce.lib.input.FileInputFormat

INPUT_DIR, INPUT_DIR_RECURSIVE, NUM_INPUT_FILES, PATHFILTER_CLASS, SPLIT_MAXSIZE, SPLIT_MINSIZE

Constructor Summary

Constructors

Constructor and Description
BGZFSplitFileInputFormat()

Method Summary

Modifier and Type	Method and Description
List<org.apache.hadoop.mapreduce.InputSplit>	getSplits(org.apache.hadoop.mapreduce.JobContext job) The splits returned are FileSplits.
boolean	isSplitable(org.apache.hadoop.mapreduce.JobContext job, org.apache.hadoop.fs.Path path)

Methods inherited from class org.apache.hadoop.mapreduce.lib.input.FileInputFormat

addInputPath, addInputPathRecursively, addInputPaths, computeSplitSize, getBlockIndex, getFormatMinSplitSize, getInputDirRecursive, getInputPathFilter, getInputPaths, getMaxSplitSize, getMinSplitSize, listStatus, makeSplit, setInputDirRecursive, setInputPathFilter, setInputPaths, setInputPaths, setMaxInputSplitSize, setMinInputSplitSize

Methods inherited from class org.apache.hadoop.mapreduce.InputFormat

createRecordReader

Methods inherited from class java.lang.Object

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

Constructor Detail

BGZFSplitFileInputFormat

public BGZFSplitFileInputFormat()

Method Detail

getSplits

public List<org.apache.hadoop.mapreduce.InputSplit> getSplits(org.apache.hadoop.mapreduce.JobContext job)
                                                       throws IOException

The splits returned are FileSplits.

Overrides:

getSplits in class org.apache.hadoop.mapreduce.lib.input.FileInputFormat<K,V>

Throws:

IOException

isSplitable

public boolean isSplitable(org.apache.hadoop.mapreduce.JobContext job,
                           org.apache.hadoop.fs.Path path)

Overrides:

isSplitable in class org.apache.hadoop.mapreduce.lib.input.FileInputFormat<K,V>