DeprecatedBAMRecordReader.java Source code

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Here is the source code for DeprecatedBAMRecordReader.java

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// 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: 2013-02-05 15:35:55

import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.LongWritable;

import org.apache.hadoop.mapred.FileSplit;
import org.apache.hadoop.mapred.InputSplit;
import org.apache.hadoop.mapred.JobConf;
import org.apache.hadoop.mapred.RecordReader;
import org.apache.hadoop.mapred.Reporter;

import net.sf.samtools.seekablestream.SeekableStream;

import fi.tkk.ics.hadoop.bam.BAMRecordReader;
import fi.tkk.ics.hadoop.bam.BAMSplitGuesser;
import fi.tkk.ics.hadoop.bam.FileVirtualSplit;
import fi.tkk.ics.hadoop.bam.SAMRecordWritable;
import fi.tkk.ics.hadoop.bam.util.WrapSeekable;

// Wraps BAMRecordReader, providing the deprecated mapred API.
public class DeprecatedBAMRecordReader implements RecordReader<LongWritable, SAMRecordWritable> {
    private final BAMRecordReader rr = new BAMRecordReader();

    private final long splitLength;

    public DeprecatedBAMRecordReader(InputSplit split, final JobConf job, Reporter reporter) throws IOException {
        if (split instanceof DeprecatedFileVirtualSplit) {
            rr.initialize(((DeprecatedFileVirtualSplit) split).vs, new FakeTaskAttemptContext(job));

            splitLength = split.getLength();
            return;

        }
        if (split instanceof FileSplit) {
            // XXX             XXX
            //     XXX     XXX
            //         XXX
            //     XXX     XXX
            // XXX             XXX
            //
            // Hive gives us its own custom FileSplits for some reason, so we have
            // to do our own split alignment. (Sometimes, anyway; for "select
            // count(*) from table" we get FileSplits here, but for "select * from
            // table" our input format is used directly. Perhaps it's only because
            // the latter doesn't spawn a MapReduce job, so getting a FileSplit
            // here is the common case.)
            //
            // Since we get only one split at a time here, this is very poor: we
            // have to open the file for every split, even if it's the same file
            // every time.
            //
            // This should always work, but might be /very/ slow. I can't think of
            // a better way.

            final FileSplit fspl = (FileSplit) split;
            final Path path = fspl.getPath();

            final long beg = fspl.getStart();
            final long end = beg + fspl.getLength();

            final SeekableStream sin = WrapSeekable.openPath(path.getFileSystem(job), path);
            final BAMSplitGuesser guesser = new BAMSplitGuesser(sin);

            final long alignedBeg = guesser.guessNextBAMRecordStart(beg, end);
            sin.close();

            if (alignedBeg == end)
                throw new IOException("Guesser found nothing after pos " + beg);

            final long alignedEnd = end << 16 | 0xffff;
            splitLength = (alignedEnd - alignedBeg) >> 16;

            rr.initialize(new FileVirtualSplit(path, alignedBeg, alignedEnd, fspl.getLocations()),
                    new FakeTaskAttemptContext(job));
            return;
        }

        throw new ClassCastException("Can only handle DeprecatedFileVirtualSplit and FileSplit");
    }

    @Override
    public void close() throws IOException {
        rr.close();
    }

    @Override
    public LongWritable createKey() {
        return new LongWritable();
    }

    @Override
    public SAMRecordWritable createValue() {
        return new SAMRecordWritable();
    }

    @Override
    public long getPos() {
        return splitLength == 0 ? 1 : (long) (getProgress() * splitLength);
    }

    @Override
    public float getProgress() {
        return rr.getProgress();
    }

    @Override
    public boolean next(LongWritable key, SAMRecordWritable value) {
        if (!rr.nextKeyValue())
            return false;
        key.set(rr.getCurrentKey().get());
        value.set(rr.getCurrentValue().get());
        return true;
    }
}