org.seqdoop.hadoop_bam

Class BAMInputFormat

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.BAMInputFormat

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

An InputFormat for BAM 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

Modifier and Type	Field and Description
static boolean	DEBUG_BAM_SPLITTER
static String	INTERVALS_PROPERTY Filter by region, like -L in SAMtools.
static String	KEEP_PAIRED_READS_TOGETHER_PROPERTY If set to true, ensure that for paired reads both reads in a pair are always in the same split for queryname-sorted BAM files.

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
BAMInputFormat()

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 BAMRecordReader initialized with the parameters.
List<org.apache.hadoop.mapreduce.InputSplit>	getSplits(org.apache.hadoop.mapreduce.JobContext job) The splits returned are FileVirtualSplits.
List<org.apache.hadoop.mapreduce.InputSplit>	getSplits(List<org.apache.hadoop.mapreduce.InputSplit> splits, org.apache.hadoop.conf.Configuration cfg)
boolean	isSplitable(org.apache.hadoop.mapreduce.JobContext job, org.apache.hadoop.fs.Path path)
static <T extends htsjdk.samtools.util.Locatable> void	setIntervals(org.apache.hadoop.conf.Configuration conf, List<T> intervals)

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

DEBUG_BAM_SPLITTER

public static final boolean DEBUG_BAM_SPLITTER

See Also:

Constant Field Values

KEEP_PAIRED_READS_TOGETHER_PROPERTY

public static final String KEEP_PAIRED_READS_TOGETHER_PROPERTY

If set to true, ensure that for paired reads both reads in a pair are always in the same split for queryname-sorted BAM files.

Note: only use this option if for all paired reads both reads in each pair are present, otherwise it is possible that reads may be silently dropped.

See Also:

Constant Field Values

INTERVALS_PROPERTY

public static final String INTERVALS_PROPERTY

Filter by region, like -L in SAMtools. Takes a comma-separated list of intervals, e.g. chr1:1-20000,chr2:12000-20000. For programmatic use setIntervals(Configuration, List) should be preferred.

See Also:

Constant Field Values

Constructor Detail

BAMInputFormat

public BAMInputFormat()

Method Detail

setIntervals

public static <T extends htsjdk.samtools.util.Locatable> void setIntervals(org.apache.hadoop.conf.Configuration conf,
                                                                           List<T> intervals)

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 BAMRecordReader initialized with the parameters.

Specified by:

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

Throws:

InterruptedException

IOException

getSplits

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

The splits returned are FileVirtualSplits.

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 cfg)
                                                       throws IOException

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