org.seqdoop.hadoop_bam

Class CRAMInputFormat

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.CRAMInputFormat

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

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

Modifier and Type	Field and Description
static String	REFERENCE_SOURCE_PATH_PROPERTY

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
CRAMInputFormat()

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 context)
List<org.apache.hadoop.mapreduce.InputSplit>	getSplits(org.apache.hadoop.mapreduce.JobContext job)
List<org.apache.hadoop.mapreduce.InputSplit>	getSplits(List<org.apache.hadoop.mapreduce.InputSplit> splits, org.apache.hadoop.conf.Configuration conf)
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 java.lang.Object

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

Field Detail

REFERENCE_SOURCE_PATH_PROPERTY

public static final String REFERENCE_SOURCE_PATH_PROPERTY

See Also:

Constant Field Values

Constructor Detail

CRAMInputFormat

public CRAMInputFormat()

Method Detail

getSplits

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

Overrides:

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

Throws:

IOException

getSplits

public List<org.apache.hadoop.mapreduce.InputSplit> getSplits(List<org.apache.hadoop.mapreduce.InputSplit> splits,
                                                              org.apache.hadoop.conf.Configuration conf)
                                                       throws IOException

Throws:

IOException

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 context)
                                                                                                                 throws IOException,
                                                                                                                        InterruptedException

Specified by:

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

Throws:

IOException

InterruptedException

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>