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/*
dsh-bio-tools Command line tools.
Copyright (c) 2013-2024 held jointly by the individual authors.
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 3 of the License, or (at
your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
> http://www.fsf.org/licensing/licenses/lgpl.html
> http://www.opensource.org/licenses/lgpl-license.php
*/
package org.dishevelled.bio.tools;
import static org.dishevelled.compress.Readers.reader;
import java.io.BufferedReader;
import java.io.File;
import java.nio.file.Path;
import java.util.List;
import javax.annotation.Nullable;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMFileWriter;
import htsjdk.samtools.SAMFileWriterFactory;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMUtils;
import htsjdk.samtools.util.SequenceUtil;
import htsjdk.samtools.util.StringUtil;
import org.biojava.bio.program.fastq.Fastq;
import org.dishevelled.bio.read.PairedEndAdapter;
import org.dishevelled.bio.read.PairedEndFastqReader;
import org.dishevelled.commandline.ArgumentList;
import org.dishevelled.commandline.CommandLine;
import org.dishevelled.commandline.CommandLineParseException;
import org.dishevelled.commandline.CommandLineParser;
import org.dishevelled.commandline.Switch;
import org.dishevelled.commandline.Usage;
import org.dishevelled.commandline.argument.FileArgument;
import org.dishevelled.commandline.argument.IntegerArgument;
import org.dishevelled.commandline.argument.PathArgument;
import org.dishevelled.commandline.argument.StringArgument;
import org.dishevelled.commandline.argument.StringListArgument;
/**
* Convert DNA sequences in interleaved FASTQ format to unaligned BAM format.
*
* @since 2.1
* @author Michael Heuer
*/
public final class InterleavedFastqToBam extends WithReadGroup {
private final Path fastqPath;
private final File bamFile;
private final SAMFileHeader header = new SAMFileHeader();
private final SAMFileWriterFactory writerFactory = new SAMFileWriterFactory();
private static final String USAGE = "dsh-interleaved-fastq-to-bam [args]";
/**
* Convert DNA sequences in interleaved FASTQ format to unaligned BAM format.
*
* @deprecated will be removed in version 3.0
* @param fastqFile input interleaved FASTQ file, if any
* @param bamFile output BAM file, if any
* @param readGroupId read group id, if any
* @param readGroupSample read group sample, if any
* @param readGroupLibrary read group library, if any
* @param readGroupPlatformUnit read group platform unit, if any
* @param readGroupInsertSize read group insert size, if any
* @param readGroupBarcodes read group barcodes, if any
*/
public InterleavedFastqToBam(@Nullable final File fastqFile,
@Nullable final File bamFile,
@Nullable final String readGroupId,
@Nullable final String readGroupSample,
@Nullable final String readGroupLibrary,
@Nullable final String readGroupPlatformUnit,
@Nullable final Integer readGroupInsertSize,
@Nullable final List readGroupBarcodes) {
this(fastqFile == null ? null : fastqFile.toPath(),
bamFile,
readGroupId,
readGroupSample,
readGroupLibrary,
readGroupPlatformUnit,
readGroupInsertSize,
readGroupBarcodes);
}
/**
* Convert DNA sequences in interleaved FASTQ format to unaligned BAM format.
*
* @since 2.1
* @param fastqPath input interleaved FASTQ path, if any
* @param bamFile output BAM file, if any
* @param readGroupId read group id, if any
* @param readGroupSample read group sample, if any
* @param readGroupLibrary read group library, if any
* @param readGroupPlatformUnit read group platform unit, if any
* @param readGroupInsertSize read group insert size, if any
* @param readGroupBarcodes read group barcodes, if any
*/
public InterleavedFastqToBam(@Nullable final Path fastqPath,
@Nullable final File bamFile,
@Nullable final String readGroupId,
@Nullable final String readGroupSample,
@Nullable final String readGroupLibrary,
@Nullable final String readGroupPlatformUnit,
@Nullable final Integer readGroupInsertSize,
@Nullable final List readGroupBarcodes) {
super(readGroupId, readGroupSample, readGroupLibrary, readGroupPlatformUnit, readGroupInsertSize, readGroupBarcodes);
this.fastqPath = fastqPath;
this.bamFile = bamFile;
// add read group to header if present
toReadGroupOpt().ifPresent(readGroup -> header.addReadGroup(readGroup));
}
@Override
public Integer call() throws Exception {
BufferedReader reader = null;
SAMFileWriter writer = null;
try {
reader = reader(fastqPath);
if (bamFile == null) {
writer = writerFactory.makeBAMWriter(header, false, System.out);
}
else {
writer = writerFactory.makeBAMWriter(header, false, bamFile);
}
final SAMFileWriter sfw = writer;
PairedEndFastqReader.streamInterleaved(reader, new PairedEndAdapter() {
@Override
public void paired(final Fastq left, final Fastq right) {
sfw.addAlignment(convertLeft(left));
sfw.addAlignment(convertRight(right));
}
});
return 0;
}
finally {
try {
reader.close();
}
catch (Exception e) {
// ignore
}
try {
writer.close();
}
catch (Exception e) {
// ignore
}
}
}
SAMRecord convertLeft(final Fastq left)
{
SAMRecord record = convert(left);
record.setReadPairedFlag(true);
record.setFirstOfPairFlag(true);
return record;
}
SAMRecord convertRight(final Fastq right)
{
SAMRecord record = convert(right);
record.setReadPairedFlag(true);
record.setSecondOfPairFlag(true);
return record;
}
private SAMRecord convert(final Fastq fastq)
{
SAMRecord record = new SAMRecord(header);
record.setReadName(SequenceUtil.getSamReadNameFromFastqHeader(fastq.getDescription()));
record.setReadBases(StringUtil.stringToBytes(fastq.getSequence()));
record.setBaseQualities(SAMUtils.fastqToPhred(fastq.getQuality()));
if (getReadGroupId() != null) {
record.setAttribute("RG", getReadGroupId());
if (getReadGroupLibrary() != null) {
record.setAttribute("LB", getReadGroupLibrary());
}
if (getReadGroupPlatformUnit() != null) {
record.setAttribute("PU", getReadGroupPlatformUnit());
}
if (getReadGroupInsertSize() != null) {
record.setInferredInsertSize(getReadGroupInsertSize());
}
}
record.setReadUnmappedFlag(true);
return record;
}
/**
* Main.
*
* @param args command line args
*/
public static void main(final String[] args) {
Switch about = new Switch("a", "about", "display about message");
Switch help = new Switch("h", "help", "display help message");
PathArgument fastqPath = new PathArgument("i", "input-fastq-path", "input interleaved FASTQ path, default stdin", false);
FileArgument bamFile = new FileArgument("o", "output-bam-file", "output BAM file, default stdout", false);
StringArgument readGroupId = createReadGroupIdArgument();
StringArgument readGroupSample = createReadGroupSampleArgument();
StringArgument readGroupLibrary = createReadGroupLibraryArgument();
StringArgument readGroupPlatformUnit = createReadGroupPlatformUnitArgument();
IntegerArgument readGroupInsertSize = createReadGroupInsertSizeArgument();
StringListArgument readGroupBarcodes = createReadGroupBarcodesArgument();
ArgumentList arguments = new ArgumentList(about, help, fastqPath, bamFile, readGroupId, readGroupSample, readGroupLibrary, readGroupPlatformUnit, readGroupInsertSize, readGroupBarcodes);
CommandLine commandLine = new CommandLine(args);
InterleavedFastqToBam interleavedFastqToBam = null;
try
{
CommandLineParser.parse(commandLine, arguments);
if (about.wasFound()) {
About.about(System.out);
System.exit(0);
}
if (help.wasFound()) {
Usage.usage(USAGE, null, commandLine, arguments, System.out);
System.exit(0);
}
interleavedFastqToBam = new InterleavedFastqToBam(fastqPath.getValue(), bamFile.getValue(), readGroupId.getValue(), readGroupSample.getValue(), readGroupLibrary.getValue(), readGroupPlatformUnit.getValue(), readGroupInsertSize.getValue(), readGroupBarcodes.getValue());
}
catch (CommandLineParseException e) {
Usage.usage(USAGE, e, commandLine, arguments, System.err);
System.exit(-1);
}
try {
System.exit(interleavedFastqToBam.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}
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