org.seqdoop.hadoop_bam

Class SAMInputFormat

java.lang.Object

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

org.apache.hadoop.mapreduce.lib.input.FileInputFormat<org.apache.hadoop.io.LongWritable,SAMRecordWritable>

org.seqdoop.hadoop_bam.SAMInputFormat

public class SAMInputFormat
extends org.apache.hadoop.mapreduce.lib.input.FileInputFormat<org.apache.hadoop.io.LongWritable,SAMRecordWritable>

An InputFormat for SAM files. Values are the individual records; see BAMRecordReader for the meaning of the key.

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
SAMInputFormat()

Method Summary

Modifier and Type	Method and Description
org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.LongWritable,SAMRecordWritable>	createRecordReader(org.apache.hadoop.mapreduce.InputSplit split, org.apache.hadoop.mapreduce.TaskAttemptContext ctx) Returns a SAMRecordReader initialized with the parameters.
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, getSplits, listStatus, makeSplit, setInputDirRecursive, setInputPathFilter, setInputPaths, setInputPaths, setMaxInputSplitSize, setMinInputSplitSize

Methods inherited from class java.lang.Object

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

Constructor Detail

SAMInputFormat

public SAMInputFormat()

Method Detail

createRecordReader

public org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.LongWritable,SAMRecordWritable> createRecordReader(org.apache.hadoop.mapreduce.InputSplit split,
                                                                                                                        org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
                                                                                                                 throws InterruptedException,
                                                                                                                        IOException

Returns a SAMRecordReader initialized with the parameters.

Specified by:

createRecordReader in class org.apache.hadoop.mapreduce.InputFormat<org.apache.hadoop.io.LongWritable,SAMRecordWritable>

Throws:

InterruptedException

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