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A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework.
// Copyright (c) 2013 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: 2013-06-26 12:47:26
package org.seqdoop.hadoop_bam;
import htsjdk.samtools.util.BlockCompressedInputStream;
import htsjdk.samtools.util.Interval;
import htsjdk.samtools.util.Locatable;
import htsjdk.tribble.index.Block;
import htsjdk.tribble.index.tabix.TabixIndex;
import htsjdk.tribble.util.TabixUtils;
import java.io.BufferedInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.compress.CompressionCodec;
import org.apache.hadoop.io.compress.CompressionCodecFactory;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.io.compress.SplittableCompressionCodec;
import org.apache.hadoop.mapreduce.JobContext;
import org.apache.hadoop.mapreduce.InputSplit;
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;
import htsjdk.samtools.seekablestream.SeekableStream;
import org.seqdoop.hadoop_bam.util.BGZFEnhancedGzipCodec;
import org.seqdoop.hadoop_bam.util.BGZFCodec;
import org.seqdoop.hadoop_bam.util.IntervalUtil;
import org.seqdoop.hadoop_bam.util.WrapSeekable;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/** An {@link org.apache.hadoop.mapreduce.InputFormat} for VCF files. Values
* are the individual records; see {@link VCFRecordReader} for the meaning of
* the key.
*/
public class VCFInputFormat
extends FileInputFormat
{
private static final Logger logger = LoggerFactory.getLogger(VCFInputFormat.class);
/** Whether file extensions are to be trusted, defaults to true.
*
* @see VCFFormat#inferFromFilePath
*/
public static final String TRUST_EXTS_PROPERTY =
"hadoopbam.vcf.trust-exts";
/**
* 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 {@link #setIntervals(Configuration, List)} should be preferred.
*/
public static final String INTERVALS_PROPERTY = "hadoopbam.vcf.intervals";
public static void setIntervals(Configuration conf,
List intervals) {
StringBuilder sb = new StringBuilder();
for (Iterator it = intervals.iterator(); it.hasNext(); ) {
Locatable l = it.next();
sb.append(String.format("%s:%d-%d", l.getContig(), l.getStart(), l.getEnd()));
if (it.hasNext()) {
sb.append(",");
}
}
conf.set(INTERVALS_PROPERTY, sb.toString());
}
static List getIntervals(Configuration conf) {
return IntervalUtil.getIntervals(conf, INTERVALS_PROPERTY);
}
private final Map formatMap;
private final boolean givenMap;
private Configuration conf;
private boolean trustExts;
/** 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
* VCFInputFormat can be used directly in
* Job.setInputFormatClass.
*/
public VCFInputFormat() {
this.formatMap = new HashMap();
this.givenMap = false;
this.conf = null;
}
/** Creates a new input format, reading {@link #TRUST_EXTS_PROPERTY} from
* the given Configuration.
*/
public VCFInputFormat(Configuration conf) {
this.formatMap = new HashMap();
this.conf = conf;
this.trustExts = conf.getBoolean(TRUST_EXTS_PROPERTY, true);
this.givenMap = false;
}
/** 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 VCFInputFormat(Map formatMap) {
this.formatMap = formatMap;
this.givenMap = true;
// Arbitrary values.
this.conf = null;
this.trustExts = false;
}
/** Returns the {@link VCFFormat} corresponding to the given path. Returns
* null if it cannot be determined even based on the file
* contents (unless future VCF/BCF formats are very different, this means
* that the path does not refer to a VCF or BCF file).
*
* If this input format was constructed using a given
* Map<Path,VCFFormat> and the path is not contained
* within that map, throws an {@link IllegalArgumentException}.
*/
public VCFFormat getFormat(final Path path) {
VCFFormat fmt = formatMap.get(path);
if (fmt != null || formatMap.containsKey(path))
return fmt;
if (givenMap)
throw new IllegalArgumentException(
"VCF format for '"+path+"' not in given map");
if (this.conf == null)
throw new IllegalStateException("Don't have a Configuration yet");
if (trustExts) {
final VCFFormat f = VCFFormat.inferFromFilePath(path);
if (f != null) {
formatMap.put(path, f);
return f;
}
}
try {
fmt = VCFFormat.inferFromData(path.getFileSystem(conf).open(path));
} catch (IOException e) {}
formatMap.put(path, fmt);
return fmt;
}
@Override
protected boolean isSplitable(JobContext context, Path filename) {
Configuration conf = context.getConfiguration();
final CompressionCodec codec =
new CompressionCodecFactory(context.getConfiguration()).getCodec(filename);
if (codec == null) {
return true;
}
if (codec instanceof BGZFCodec || codec instanceof BGZFEnhancedGzipCodec) {
boolean splittable;
try {
try (FSDataInputStream in = filename.getFileSystem(conf).open(filename)) {
splittable = BlockCompressedInputStream.isValidFile(new BufferedInputStream(in));
}
} catch (IOException e) {
// can't determine if BGZF or GZIP, conservatively assume latter
splittable = false;
}
if (!splittable) {
logger.warn("{} is not splittable, consider using block-compressed gzip (BGZF)", filename);
}
return splittable;
} else if (codec instanceof GzipCodec) {
logger.warn("Using GzipCodec, which is not splittable, consider using block compressed gzip (BGZF) and BGZFCodec/BGZFEnhancedGzipCodec.");
}
return codec instanceof SplittableCompressionCodec;
}
/** Returns a {@link BCFRecordReader} or {@link VCFRecordReader} as
* appropriate, initialized with the given parameters.
*
* Throws {@link IllegalArgumentException} if the given input split is
* not a {@link FileVirtualSplit} or a {@link FileSplit}, or if the path
* referred to is not recognized as a VCF or BCF 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 VCFFormat fmt = getFormat(path);
if (fmt == null)
throw new IllegalArgumentException(
"unknown VCF format, cannot create RecordReader: "+path);
final RecordReader rr;
switch (fmt) {
case VCF: rr = new VCFRecordReader(); break;
case BCF: rr = new BCFRecordReader(); break;
default: assert false; return null;
}
rr.initialize(split, ctx);
return rr;
}
/** Defers to {@link BCFSplitGuesser} as appropriate for each individual
* path. VCF 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 = super.getSplits(job);
// We have to partition the splits by input format and hand the BCF ones
// over to getBCFSplits().
final List
bcfOrigSplits = new ArrayList(origSplits.size());
final List
newSplits = new ArrayList(origSplits.size());
for (final InputSplit iSplit : origSplits) {
final FileSplit split = (FileSplit)iSplit;
if (VCFFormat.BCF.equals(getFormat(split.getPath())))
bcfOrigSplits.add(split);
else
newSplits.add(split);
}
fixBCFSplits(bcfOrigSplits, newSplits);
return filterByInterval(newSplits, conf);
}
// The given FileSplits should all be for BCF files. Adds InputSplits
// aligned to record boundaries. Compressed BCF results in
// FileVirtualSplits, uncompressed in FileSplits.
private void fixBCFSplits(
List splits, List newSplits)
throws IOException
{
// addGuessedSplits() requires the given splits to be sorted by file
// path, so do so. Although FileInputFormat.getSplits() does, at the time
// of writing this, generate them in that order, we shouldn't rely on it.
Collections.sort(splits, new Comparator() {
public int compare(FileSplit a, FileSplit b) {
return a.getPath().compareTo(b.getPath());
}
});
for (int i = 0; i < splits.size();)
i = addGuessedSplits(splits, i, newSplits);
}
// Handles all the splits that share the Path of the one at index i,
// returning the next index to be used.
private int addGuessedSplits(
List splits, int i, List newSplits)
throws IOException
{
final Path path = splits.get(i).getPath();
final SeekableStream sin = WrapSeekable.openPath(conf, path);
final BCFSplitGuesser guesser = new BCFSplitGuesser(sin);
final boolean isBGZF = guesser.isBGZF();
InputSplit prevSplit = null;
for (; i < splits.size(); ++i) {
final FileSplit fspl = splits.get(i);
if (!fspl.getPath().equals(path))
break;
final String[] locs = fspl.getLocations();
final long beg = fspl.getStart();
final long end = beg + fspl.getLength();
final long alignBeg = guesser.guessNextBCFRecordStart(beg, end);
// As the guesser goes to the next BGZF block before looking for BCF
// records, the ending BGZF blocks have to always be traversed fully.
// Hence force the length to be 0xffff, the maximum possible.
final long alignEnd = isBGZF ? end << 16 | 0xffff : end;
final long length = alignEnd - alignBeg;
if (alignBeg == end) {
// No records detected in this split: merge it to the previous one.
// This could legitimately happen e.g. if we have a split that is
// so small that it only contains the middle part of a BGZF block.
//
// Of course, if it's the first split, then this is simply not a
// valid BCF file.
//
// FIXME: In theory, any number of splits could only contain parts
// of the BCF header before we start to see splits that contain BCF
// records. For now, we require that the split size is at least as
// big as the header and don't handle that case.
if (prevSplit == null)
throw new IOException("'" + path + "': no records in first "+
"split: bad BCF file or tiny split size?");
if (isBGZF) {
((FileVirtualSplit)prevSplit).setEndVirtualOffset(alignEnd);
continue;
}
prevSplit = new FileSplit(path, alignBeg, length, locs);
newSplits.remove(newSplits.size() - 1);
} else {
prevSplit =
isBGZF ? new FileVirtualSplit(path, alignBeg, alignEnd, locs)
: new FileSplit (path, alignBeg, length, locs);
}
newSplits.add(prevSplit);
}
sin.close();
return i;
}
private List filterByInterval(List splits, Configuration conf)
throws IOException {
List intervals = getIntervals(conf);
if (intervals == null) {
return splits;
}
List blocks = new ArrayList<>();
Set vcfFiles = new LinkedHashSet();
for (InputSplit split : splits) {
if (split instanceof FileSplit) {
vcfFiles.add(((FileSplit) split).getPath());
} else if (split instanceof FileVirtualSplit) {
vcfFiles.add(((FileVirtualSplit) split).getPath());
} else {
throw new IllegalArgumentException(
"split '"+split+"' has unknown type: cannot extract path");
}
}
for (Path vcfFile : vcfFiles) {
Path indexFile = vcfFile.suffix(TabixUtils.STANDARD_INDEX_EXTENSION);
FileSystem fs = vcfFile.getFileSystem(conf);
if (!fs.exists(indexFile)) {
logger.warn(
"No tabix index file found for {}, splits will not be filtered, which may be very inefficient",
indexFile);
return splits;
}
try (InputStream in = new BlockCompressedInputStream(fs.open(indexFile))) {
TabixIndex index = new TabixIndex(in);
for (Locatable interval : intervals) {
String contig = interval.getContig();
int intervalStart = interval.getStart();
int intervalEnd = interval.getEnd();
blocks.addAll(index.getBlocks(contig, intervalStart, intervalEnd));
}
}
}
// Use the blocks to filter the splits
List filteredSplits = new ArrayList();
for (InputSplit split : splits) {
if (split instanceof FileSplit) {
FileSplit fileSplit = (FileSplit) split;
long splitStart = fileSplit.getStart() << 16;
long splitEnd = (fileSplit.getStart() + fileSplit.getLength()) << 16;
// if any block overlaps with the split, keep the split, but don't adjust its size
// as the BGZF block decompression is handled by BGZFCodec, not by the reader
// directly
for (Block block : blocks) {
long blockStart = block.getStartPosition();
long blockEnd = block.getEndPosition();
if (overlaps(splitStart, splitEnd, blockStart, blockEnd)) {
filteredSplits.add(split);
break;
}
}
} else {
FileVirtualSplit virtualSplit = (FileVirtualSplit) split;
long splitStart = virtualSplit.getStartVirtualOffset();
long splitEnd = virtualSplit.getEndVirtualOffset();
// if any block overlaps with the split, keep the split, but adjust the start and
// end to the maximally overlapping portion for all blocks that overlap
long newStart = Long.MAX_VALUE;
long newEnd = Long.MIN_VALUE;
boolean overlaps = false;
for (Block block : blocks) {
long blockStart = block.getStartPosition();
long blockEnd = block.getEndPosition();
if (overlaps(splitStart, splitEnd, blockStart, blockEnd)) {
long overlapStart = Math.max(splitStart, blockStart);
long overlapEnd = Math.min(splitEnd, blockEnd);
newStart = Math.min(newStart, overlapStart);
newEnd = Math.max(newEnd, overlapEnd);
overlaps = true;
}
}
if (overlaps) {
filteredSplits.add(new FileVirtualSplit(virtualSplit.getPath(), newStart, newEnd,
virtualSplit.getLocations()));
}
}
}
return filteredSplits;
}
private static boolean overlaps(long start, long end, long start2, long end2) {
return (start2 >= start && start2 <= end) || (end2 >=start && end2 <= end) ||
(start >= start2 && end <= end2);
}
}