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 String	BOUNDED_TRAVERSAL_PROPERTY If set to true, only include reads that overlap the given intervals (if specified), and unplaced unmapped reads (if specified).
static String	ENABLE_BAI_SPLIT_CALCULATOR If set to true, enables the use of BAM indices to calculate splits.
static String	INTERVALS_PROPERTY Filter by region, like -L in SAMtools.
static String	TRAVERSE_UNPLACED_UNMAPPED_PROPERTY If set to true, include unplaced unmapped reads (that is, unmapped reads with no position).

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 void	setEnableBAISplitCalculator(org.apache.hadoop.conf.Configuration conf, boolean setEnabled) Enables or disables the split calculator that uses the BAM index to calculate splits.
static <T extends htsjdk.samtools.util.Locatable> void	setIntervals(org.apache.hadoop.conf.Configuration conf, List<T> intervals) Only include reads that overlap the given intervals.
static <T extends htsjdk.samtools.util.Locatable> void	setTraversalParameters(org.apache.hadoop.conf.Configuration conf, List<T> intervals, boolean traverseUnplacedUnmapped) Only include reads that overlap the given intervals (if specified) and unplaced unmapped reads (if true).
static void	unsetTraversalParameters(org.apache.hadoop.conf.Configuration conf) Reset traversal parameters so that all reads are included.

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

BOUNDED_TRAVERSAL_PROPERTY

public static final String BOUNDED_TRAVERSAL_PROPERTY

If set to true, only include reads that overlap the given intervals (if specified), and unplaced unmapped reads (if specified). For programmatic use setTraversalParameters(Configuration, List, boolean) should be preferred.

See Also:

Constant Field Values

ENABLE_BAI_SPLIT_CALCULATOR

public static final String ENABLE_BAI_SPLIT_CALCULATOR

If set to true, enables the use of BAM indices to calculate splits. For programmatic use setEnableBAISplitCalculator(Configuration, boolean) should be preferred. By default, this split calculator is disabled in favor of the splitting-bai calculator.

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

TRAVERSE_UNPLACED_UNMAPPED_PROPERTY

public static final String TRAVERSE_UNPLACED_UNMAPPED_PROPERTY

If set to true, include unplaced unmapped reads (that is, unmapped reads with no position). For programmatic use setTraversalParameters(Configuration, List, boolean) 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)

Only include reads that overlap the given intervals. Unplaced unmapped reads are not included.

Type Parameters:

T - the Locatable type

Parameters:

conf - the Hadoop configuration to set properties on

intervals - the intervals to filter by

setEnableBAISplitCalculator

public static void setEnableBAISplitCalculator(org.apache.hadoop.conf.Configuration conf,
                                               boolean setEnabled)

Enables or disables the split calculator that uses the BAM index to calculate splits.

setTraversalParameters

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

Only include reads that overlap the given intervals (if specified) and unplaced unmapped reads (if true).

Type Parameters:

T - the Locatable type

Parameters:

conf - the Hadoop configuration to set properties on

intervals - the intervals to filter by, or null if all reads are to be included (in which case traverseUnplacedUnmapped must be true)

traverseUnplacedUnmapped - whether to included unplaced unampped reads

unsetTraversalParameters

public static void unsetTraversalParameters(org.apache.hadoop.conf.Configuration conf)

Reset traversal parameters so that all reads are included.

Parameters:

conf - the Hadoop configuration to set properties on

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>