Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
/*
* 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.FileExtensions;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.RuntimeIOException;
import htsjdk.samtools.util.zip.DeflaterFactory;
import java.io.File;
import java.io.IOException;
import java.io.OutputStream;
import java.io.StringWriter;
import java.io.Writer;
import java.nio.file.Files;
import java.nio.file.Path;
/**
* Concrete implementation of SAMFileWriter for writing gzipped BAM files.
*/
public 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(blockCompressedOutputStream);
outputBinaryCodec.setOutputFileName(path.getAbsolutePath());
}
protected BAMFileWriter(final File path, final int compressionLevel) {
blockCompressedOutputStream = new BlockCompressedOutputStream(path, compressionLevel);
outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
outputBinaryCodec.setOutputFileName(path.getAbsolutePath());
}
protected BAMFileWriter(final OutputStream os, final File file) {
blockCompressedOutputStream = new BlockCompressedOutputStream(os, file);
outputBinaryCodec = new BinaryCodec(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(blockCompressedOutputStream);
outputBinaryCodec.setOutputFileName(getPathString(file));
}
protected BAMFileWriter(final OutputStream os, final File file, final int compressionLevel, final DeflaterFactory deflaterFactory) {
blockCompressedOutputStream = new BlockCompressedOutputStream(os, file, compressionLevel, deflaterFactory);
outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
outputBinaryCodec.setOutputFileName(getPathString(file));
}
protected BAMFileWriter(final OutputStream os, final String absoluteFilename, final int compressionLevel, final DeflaterFactory deflaterFactory) {
blockCompressedOutputStream = new BlockCompressedOutputStream(os, (Path)null, compressionLevel, deflaterFactory);
outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
outputBinaryCodec.setOutputFileName(absoluteFilename);
}
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 pathURI) {
try {
final String indexFileBase = pathURI.endsWith(FileExtensions.BAM) ?
pathURI.substring(0, pathURI.lastIndexOf('.')) : pathURI;
final Path indexPath = IOUtil.getPath(indexFileBase + FileExtensions.BAI_INDEX);
if (Files.exists(indexPath)) {
if (!Files.isWritable(indexPath)) {
throw new SAMException("Not creating BAM index since unable to write index file " + indexPath.toUri());
}
}
return new BAMIndexer(indexPath, getFileHeader());
} catch (Exception e) {
throw new SAMException("Not creating BAM index", e);
}
}
@Override
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);
}
}
@Override
protected void writeHeader(final String textHeader) {
writeHeader(outputBinaryCodec, getFileHeader(), textHeader);
}
@Override
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 in URI format, or null if this writer does not correspond to a file.
* To get a Path from this, use: IOUtil.getPath(getFilename()) */
@Override
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.
*/
protected static void writeHeader(final BinaryCodec outputBinaryCodec, final SAMFileHeader samFileHeader) {
final Writer stringWriter = new StringWriter();
new SAMTextHeaderCodec().encode(stringWriter, samFileHeader, true);
final String headerString = stringWriter.toString();
writeHeader(outputBinaryCodec, samFileHeader, headerString);
}
/**
* Write a BAM file header to an output stream in block compressed BAM format.
* @param outputStream the stream to write the BAM header to
* @param samFileHeader the header to write
*/
public static void writeHeader(final OutputStream outputStream, final SAMFileHeader samFileHeader) {
final BlockCompressedOutputStream blockCompressedOutputStream = new BlockCompressedOutputStream(outputStream, (Path)null);
final BinaryCodec outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
writeHeader(outputBinaryCodec, samFileHeader);
try {
blockCompressedOutputStream.flush();
} catch (final IOException ioe) {
throw new RuntimeIOException(ioe);
}
}
}
