org.seqdoop.hadoop_bam

Class FastaInputFormat

java.lang.Object

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

org.apache.hadoop.mapreduce.lib.input.FileInputFormat<org.apache.hadoop.io.Text,ReferenceFragment>

org.seqdoop.hadoop_bam.FastaInputFormat

public class FastaInputFormat
extends org.apache.hadoop.mapreduce.lib.input.FileInputFormat<org.apache.hadoop.io.Text,ReferenceFragment>

Reads the FASTA reference sequence format. Key: sequence description and position offset, delimited by ':' characters. Value: a ReferenceFragment object representing the entry. Note: here sections in the input file are assumed to be delimited by single line descriptions that start with '>'.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	FastaInputFormat.FastaRecordReader

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 Charset	UTF8

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
FastaInputFormat()

Method Summary

Modifier and Type	Method and Description
org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,ReferenceFragment>	createRecordReader(org.apache.hadoop.mapreduce.InputSplit genericSplit, org.apache.hadoop.mapreduce.TaskAttemptContext context)
List<org.apache.hadoop.mapreduce.InputSplit>	getSplits(org.apache.hadoop.mapreduce.JobContext job)
boolean	isSplitable(org.apache.hadoop.mapreduce.JobContext context, 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

UTF8

public static final Charset UTF8

Constructor Detail

FastaInputFormat

public FastaInputFormat()

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.Text,ReferenceFragment>

Throws:

IOException

isSplitable

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

Overrides:

isSplitable in class org.apache.hadoop.mapreduce.lib.input.FileInputFormat<org.apache.hadoop.io.Text,ReferenceFragment>

createRecordReader

public org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,ReferenceFragment> createRecordReader(org.apache.hadoop.mapreduce.InputSplit genericSplit,
                                                                                                                org.apache.hadoop.mapreduce.TaskAttemptContext context)
                                                                                                         throws IOException,
                                                                                                                InterruptedException

Specified by:

createRecordReader in class org.apache.hadoop.mapreduce.InputFormat<org.apache.hadoop.io.Text,ReferenceFragment>

Throws:

IOException

InterruptedException