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A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework.
// Copyright (c) 2012 Aalto University
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to
// deal in the Software without restriction, including without limitation the
// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
// sell copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
// IN THE SOFTWARE.
// File created: 2012-02-22 20:40:39
package org.seqdoop.hadoop_bam;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.fs.PathNotFoundException;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.mapreduce.InputSplit;
import org.apache.hadoop.mapreduce.JobContext;
import org.apache.hadoop.mapreduce.RecordReader;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
import org.apache.hadoop.mapreduce.lib.input.FileSplit;
/** An {@link org.apache.hadoop.mapreduce.InputFormat} for SAM, BAM, and CRAM files.
* Values are the individual records; see {@link BAMRecordReader} for the
* meaning of the key.
*
* By default, files are recognized as SAM, BAM, or CRAM based on their file
* extensions: see {@link #TRUST_EXTS_PROPERTY}. If that fails, or this
* behaviour is disabled, the first byte of each file is read to determine the
* file type.
*/
public class AnySAMInputFormat
extends FileInputFormat
{
/** A Boolean property: are file extensions trusted? The default is
* true.
*
* @see SAMFormat#inferFromFilePath
*/
public static final String TRUST_EXTS_PROPERTY =
"hadoopbam.anysam.trust-exts";
private final BAMInputFormat bamIF = new BAMInputFormat();
private final CRAMInputFormat cramIF = new CRAMInputFormat();
private final SAMInputFormat samIF = new SAMInputFormat();
private final Map formatMap;
private final boolean givenMap;
private Configuration conf;
/** Creates a new input format, which will use the
* Configuration from the first public method called. Thus this
* will behave as though constructed with a Configuration
* directly, but only after it has received it in
* createRecordReader (via the TaskAttemptContext)
* or isSplitable or getSplits (via the
* JobContext). Until then, other methods will throw an {@link
* IllegalStateException}.
*
* This constructor exists mainly as a convenience, e.g. so that
* AnySAMInputFormat can be used directly in
* Job.setInputFormatClass.
*/
public AnySAMInputFormat() {
this(null, new HashMap<>(), false);
}
/** Creates a new input format, reading {@link #TRUST_EXTS_PROPERTY} from
* the given Configuration.
*/
public AnySAMInputFormat(Configuration conf) {
this(conf, new HashMap<>(), false);
}
private static boolean trustExtensions(Configuration conf) {
return conf.getBoolean(TRUST_EXTS_PROPERTY, true);
}
/** Creates a new input format, trusting the given Map to
* define the file-to-format associations. Neither file paths nor their
* contents are looked at, only the Map is used.
*
* The Map is not copied, so it should not be modified while
* this input format is in use!
* */
public AnySAMInputFormat(Map formatMap) {
this(null, formatMap, true);
}
private AnySAMInputFormat(Configuration conf, Map formatMap, boolean givenMap){
this.formatMap = formatMap;
this.givenMap = givenMap;
this.conf = conf;
}
/** Returns the {@link SAMFormat} corresponding to the given path. Returns
* null if it cannot be determined even based on the file
* contents (unless future SAM/BAM formats are very different, this means
* that the path does not refer to a SAM or BAM file).
*
* If this input format was constructed using a given
* Map<Path,SAMFormat> and the path is not contained
* within that map, throws an {@link IllegalArgumentException}.
*/
public SAMFormat getFormat(final Path path) throws PathNotFoundException {
SAMFormat fmt = formatMap.get(path);
if (fmt != null || formatMap.containsKey(path))
return fmt;
if (givenMap)
throw new IllegalArgumentException(
"SAM format for '"+path+"' not in given map");
if (this.conf == null)
throw new IllegalStateException("Don't have a Configuration yet");
if (trustExtensions(conf)) {
final SAMFormat f = SAMFormat.inferFromFilePath(path);
if (f != null) {
formatMap.put(path, f);
return f;
}
}
try {
FileSystem fileSystem = path.getFileSystem(conf);
if (!fileSystem.exists(path)) {
throw new PathNotFoundException(path.toString());
}
fmt = SAMFormat.inferFromData(fileSystem.open(path));
} catch (IOException e) {}
formatMap.put(path, fmt);
return fmt;
}
/** Returns a {@link BAMRecordReader} or {@link SAMRecordReader} as
* appropriate, initialized with the given parameters.
*
* Throws {@link IllegalArgumentException} if the given input split is
* not a {@link FileVirtualSplit} (used by {@link BAMInputFormat}) or a
* {@link FileSplit} (used by {@link SAMInputFormat}), or if the path
* referred to is not recognized as a SAM, BAM, or CRAM file (see {@link
* #getFormat}).
*/
@Override public RecordReader
createRecordReader(InputSplit split, TaskAttemptContext ctx)
throws InterruptedException, IOException
{
final Path path;
if (split instanceof FileSplit)
path = ((FileSplit)split).getPath();
else if (split instanceof FileVirtualSplit)
path = ((FileVirtualSplit)split).getPath();
else
throw new IllegalArgumentException(
"split '"+split+"' has unknown type: cannot extract path");
if (this.conf == null)
this.conf = ctx.getConfiguration();
final SAMFormat fmt = getFormat(path);
if (fmt == null)
throw new IllegalArgumentException(
"unknown SAM format, cannot create RecordReader: "+path);
switch (fmt) {
case SAM: return samIF.createRecordReader(split, ctx);
case BAM: return bamIF.createRecordReader(split, ctx);
case CRAM: return cramIF.createRecordReader(split, ctx);
default: assert false; return null;
}
}
/** Defers to {@link BAMInputFormat}, {@link CRAMInputFormat}, or
* {@link SAMInputFormat} as appropriate for the given path.
*/
@Override public boolean isSplitable(JobContext job, Path path) {
if (this.conf == null)
this.conf = job.getConfiguration();
try {
final SAMFormat fmt = getFormat(path);
if (fmt == null)
return super.isSplitable(job, path);
switch (fmt) {
case SAM: return samIF.isSplitable(job, path);
case BAM: return bamIF.isSplitable(job, path);
case CRAM: return cramIF.isSplitable(job, path);
default: assert false; return false;
}
} catch (PathNotFoundException e) {
return super.isSplitable(job, path);
}
}
/** Defers to {@link BAMInputFormat} or {@link CRAMInputFormat} as appropriate for each
* individual path. SAM paths do not require special handling, so their splits are left
* unchanged.
*/
@Override public List getSplits(JobContext job)
throws IOException
{
if (this.conf == null)
this.conf = job.getConfiguration();
final List origSplits =
BAMInputFormat.removeIndexFiles(super.getSplits(job));
// We have to partition the splits by input format and hand them over to
// the *InputFormats for any further handling.
//
// BAMInputFormat and CRAMInputFormat need to change the split boundaries, so we can
// just extract the BAM and CRAM ones and leave the rest as they are.
final List
bamOrigSplits = new ArrayList(origSplits.size()),
cramOrigSplits = new ArrayList(origSplits.size()),
newSplits = new ArrayList(origSplits.size());
for (final InputSplit iSplit : origSplits) {
final FileSplit split = (FileSplit)iSplit;
if (SAMFormat.BAM.equals(getFormat(split.getPath())))
bamOrigSplits.add(split);
else if (SAMFormat.CRAM.equals(getFormat(split.getPath())))
cramOrigSplits.add(split);
else
newSplits.add(split);
}
newSplits.addAll(bamIF.getSplits(bamOrigSplits, job.getConfiguration()));
newSplits.addAll(cramIF.getSplits(cramOrigSplits, job.getConfiguration()));
return newSplits;
}
}