// 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<LongWritable,VariantContextWritable> { 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 <code>-L</code> in SAMtools. Takes a comma-separated * list of intervals, e.g. <code>chr1:1-20000,chr2:12000-20000</code>. For * programmatic use {@link #setIntervals(Configuration, List)} should be preferred. */ public static final String INTERVALS_PROPERTY = "hadoopbam.vcf.intervals"; public static <T extends Locatable> void setIntervals(Configuration conf, List<T> intervals) { StringBuilder sb = new StringBuilder(); for (Iterator<T> 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<Interval> getIntervals(Configuration conf) { return IntervalUtil.getIntervals(conf, INTERVALS_PROPERTY); } private final Map<Path,VCFFormat> formatMap; private final boolean givenMap; private Configuration conf; private boolean trustExts; /** Creates a new input format, which will use the * <code>Configuration</code> from the first public method called. Thus this * will behave as though constructed with a <code>Configuration</code> * directly, but only after it has received it in * <code>createRecordReader</code> (via the <code>TaskAttemptContext</code>) * or <code>isSplitable</code> or <code>getSplits</code> (via the * <code>JobContext</code>). Until then, other methods will throw an {@link * IllegalStateException}. * * This constructor exists mainly as a convenience, e.g. so that * <code>VCFInputFormat</code> can be used directly in * <code>Job.setInputFormatClass</code>. */ public VCFInputFormat() { this.formatMap = new HashMap<Path,VCFFormat>(); this.givenMap = false; this.conf = null; } /** Creates a new input format, reading {@link #TRUST_EXTS_PROPERTY} from * the given <code>Configuration</code>. */ public VCFInputFormat(Configuration conf) { this.formatMap = new HashMap<Path,VCFFormat>(); this.conf = conf; this.trustExts = conf.getBoolean(TRUST_EXTS_PROPERTY, true); this.givenMap = false; } /** Creates a new input format, trusting the given <code>Map</code> to * define the file-to-format associations. Neither file paths nor their * contents are looked at, only the <code>Map</code> is used. * * <p>The <code>Map</code> is not copied, so it should not be modified while * this input format is in use!</p> * */ public VCFInputFormat(Map<Path,VCFFormat> 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 * <code>null</code> 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). * * <p>If this input format was constructed using a given * <code>Map<Path,VCFFormat></code> and the path is not contained * within that map, throws an {@link IllegalArgumentException}.</p> */ 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(InputStream is = path.getFileSystem(conf).open(path)) { fmt = VCFFormat.inferFromData(is); } 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. * * <p>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}).</p> */ @Override public RecordReader<LongWritable,VariantContextWritable> 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<LongWritable, VariantContextWritable> 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<InputSplit> getSplits(JobContext job) throws IOException { if (this.conf == null) this.conf = job.getConfiguration(); final List<InputSplit> origSplits = super.getSplits(job); // We have to partition the splits by input format and hand the BCF ones // over to getBCFSplits(). final List<FileSplit> bcfOrigSplits = new ArrayList<FileSplit>(origSplits.size()); final List<InputSplit> newSplits = new ArrayList<InputSplit>(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<FileSplit> splits, List<InputSplit> 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<FileSplit>() { 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<FileSplit> splits, int i, List<InputSplit> 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<InputSplit> filterByInterval(List<InputSplit> splits, Configuration conf) throws IOException { List<Interval> intervals = getIntervals(conf); if (intervals == null) { return splits; } List<Block> blocks = new ArrayList<>(); Set<Path> vcfFiles = new LinkedHashSet<Path>(); 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<InputSplit> filteredSplits = new ArrayList<InputSplit>(); 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); } }