BAMFileWriter.java

/*
 * The MIT License
 *
 * Copyright (c) 2009 The Broad Institute
 *
 * 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.
 */
package htsjdk.samtools;

import htsjdk.samtools.util.BinaryCodec;
import htsjdk.samtools.util.BlockCompressedOutputStream;
import htsjdk.samtools.util.RuntimeIOException;

import java.io.DataOutputStream;
import java.io.File;
import java.io.IOException;
import java.io.OutputStream;
import java.io.StringWriter;
import java.io.Writer;

/**
 * Concrete implementation of SAMFileWriter for writing gzipped BAM files.
 */
class BAMFileWriter extends SAMFileWriterImpl {

    private final BinaryCodec outputBinaryCodec;
    private BAMRecordCodec bamRecordCodec = null;
    private final BlockCompressedOutputStream blockCompressedOutputStream;
    private BAMIndexer bamIndexer = null;

    protected BAMFileWriter(final File path) {
        blockCompressedOutputStream = new BlockCompressedOutputStream(path);
        outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
        outputBinaryCodec.setOutputFileName(path.getAbsolutePath());
    }

    protected BAMFileWriter(final File path, final int compressionLevel) {
        blockCompressedOutputStream = new BlockCompressedOutputStream(path, compressionLevel);
        outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
        outputBinaryCodec.setOutputFileName(path.getAbsolutePath());
    }

    protected BAMFileWriter(final OutputStream os, final File file) {
        blockCompressedOutputStream = new BlockCompressedOutputStream(os, file);
        outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
        outputBinaryCodec.setOutputFileName(getPathString(file));
    }

    protected BAMFileWriter(final OutputStream os, final File file, final int compressionLevel) {
        blockCompressedOutputStream = new BlockCompressedOutputStream(os, file, compressionLevel);
        outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
        outputBinaryCodec.setOutputFileName(getPathString(file));
    }

    private void prepareToWriteAlignments() {
        if (bamRecordCodec == null) {
            bamRecordCodec = new BAMRecordCodec(getFileHeader());
            bamRecordCodec.setOutputStream(outputBinaryCodec.getOutputStream(), getFilename());
        }
    }

    /** @return absolute path, or null if arg is null.  */
    private String getPathString(final File path){
        return (path != null) ? path.getAbsolutePath() : null;
    }

   // Allow enabling the bam index construction
   // only enabled by factory method before anything is written
   void enableBamIndexConstruction () {
        if (!getSortOrder().equals(SAMFileHeader.SortOrder.coordinate)){
           throw new SAMException("Not creating BAM index since not sorted by coordinates: " + getSortOrder());
        }
        if(getFilename() == null){
            throw new SAMException("Not creating BAM index since we don't have an output file name");
        }
        bamIndexer = createBamIndex(getFilename());
    }

    private BAMIndexer createBamIndex(final String path) {
        try {
            final String indexFileBase = path.endsWith(BamFileIoUtils.BAM_FILE_EXTENSION) ?
                    path.substring(0, path.lastIndexOf(".")) : path;
            final File indexFile = new File(indexFileBase + BAMIndex.BAMIndexSuffix);
            if (indexFile.exists()) {
                if (!indexFile.canWrite()) {
                    throw new SAMException("Not creating BAM index since unable to write index file " + indexFile);
                }
            }
            return new BAMIndexer(indexFile, getFileHeader());
        } catch (Exception e) {
            throw new SAMException("Not creating BAM index", e);
        }
    }

    protected void writeAlignment(final SAMRecord alignment) {
        prepareToWriteAlignments();

        if (bamIndexer != null) {
            try {
                final long startOffset = blockCompressedOutputStream.getFilePointer();
                bamRecordCodec.encode(alignment);
                final long stopOffset = blockCompressedOutputStream.getFilePointer();
                // set the alignment's SourceInfo and then prepare its index information
                alignment.setFileSource(new SAMFileSource(null, new BAMFileSpan(new Chunk(startOffset, stopOffset))));
                bamIndexer.processAlignment(alignment);
            } catch (Exception e) {
                bamIndexer = null;
                throw new SAMException("Exception when processing alignment for BAM index " + alignment, e);
            }
        } else {
            bamRecordCodec.encode(alignment);
        }
    }

    protected void writeHeader(final String textHeader) {
        writeHeader(outputBinaryCodec, getFileHeader(), textHeader);
    }

    protected void finish() {
        outputBinaryCodec.close();
            try {
                if (bamIndexer != null) {
                    bamIndexer.finish();
                }
            } catch (Exception e) {
                throw new SAMException("Exception writing BAM index file", e);
            }
    }

    /** @return absolute path, or null if this writer does not correspond to a file.  */
    protected String getFilename() {
        return outputBinaryCodec.getOutputFileName();
    }

    /**
     * Writes a header to a BAM file. samFileHeader and headerText are redundant - one can be used to regenerate the other but in
     * some instances we already have both so this allows us to save some cycles
     */
    protected static void writeHeader(final BinaryCodec outputBinaryCodec, final SAMFileHeader samFileHeader, final String headerText) {
        outputBinaryCodec.writeBytes(BAMFileConstants.BAM_MAGIC);

        // calculate and write the length of the SAM file header text and the header text
        outputBinaryCodec.writeString(headerText, true, false);

        // write the sequences binarily.  This is redundant with the text header
        outputBinaryCodec.writeInt(samFileHeader.getSequenceDictionary().size());
        for (final SAMSequenceRecord sequenceRecord: samFileHeader.getSequenceDictionary().getSequences()) {
            outputBinaryCodec.writeString(sequenceRecord.getSequenceName(), true, true);
            outputBinaryCodec.writeInt(sequenceRecord.getSequenceLength());
        }
    }

    /**
     * Writes a header to a BAM file. Might need to regenerate the String version of the header, if one already has both the
     * samFileHeader and the String, use the version of this method which takes both.
     */
    protected static void writeHeader(final BinaryCodec outputBinaryCodec, final SAMFileHeader samFileHeader) {
        // Do not use SAMFileHeader.getTextHeader() as it is not updated when changes to the underlying object are made
        final String headerString;
        final Writer stringWriter = new StringWriter();
        new SAMTextHeaderCodec().encode(stringWriter, samFileHeader, true);
        headerString = stringWriter.toString();

        writeHeader(outputBinaryCodec, samFileHeader, headerString);
    }

    protected static void writeHeader(final OutputStream outputStream, final SAMFileHeader samFileHeader) {
        final BlockCompressedOutputStream blockCompressedOutputStream = new BlockCompressedOutputStream(outputStream, null);
        final BinaryCodec outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
        writeHeader(outputBinaryCodec, samFileHeader);
        try {
            blockCompressedOutputStream.flush();
        } catch (final IOException ioe) {
            throw new RuntimeIOException(ioe);
        }
    }
}