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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 static org.dishevelled.compress.Writers.writer;
import java.io.File;
import java.io.PrintWriter;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.concurrent.Callable;
import org.dishevelled.bio.variant.vcf.VcfGenotype;
import org.dishevelled.bio.variant.vcf.VcfHeader;
import org.dishevelled.bio.variant.vcf.VcfReader;
import org.dishevelled.bio.variant.vcf.VcfRecord;
import org.dishevelled.bio.variant.vcf.VcfSample;
import org.dishevelled.bio.variant.vcf.VcfWriter;
import org.dishevelled.bio.variant.vcf.VcfStreamAdapter;
import org.dishevelled.bio.variant.vcf.header.VcfHeaderLineType;
import org.dishevelled.bio.variant.vcf.header.VcfHeaderLines;
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.PathArgument;
/**
* Remap PS Type=String phase set ids in VCF format to PS Type=Integer.
*
* @author Michael Heuer
*/
public final class RemapPhaseSet implements Callable {
private final Path inputVcfPath;
private final File outputVcfFile;
private static final String USAGE = "dsh-remap-phase-set -i input.vcf.gz -o output.vcf.gz";
/**
* Remap Type=String PS phase set ids in VCF format to Type=Integer.
*
* @deprecated will be removed in version 3.0
* @param inputVcfFile input VCF file, if any
* @param outputVcfFile output VCF file, if any
*/
public RemapPhaseSet(final File inputVcfFile, final File outputVcfFile) {
this(inputVcfFile == null ? null : inputVcfFile.toPath(), outputVcfFile);
}
/**
* Remap Type=String PS phase set ids in VCF format to Type=Integer.
*
* @since 2.1
* @param inputVcfPath input VCF path, if any
* @param outputVcfFile output VCF file, if any
*/
public RemapPhaseSet(final Path inputVcfPath, final File outputVcfFile) {
this.inputVcfPath = inputVcfPath;
this.outputVcfFile = outputVcfFile;
}
@Override
public Integer call() throws Exception {
PrintWriter writer = null;
try {
writer = writer(outputVcfFile);
final PrintWriter w = writer;
VcfReader.stream(reader(inputVcfPath), new VcfStreamAdapter() {
private boolean wroteSamples = false;
private boolean remapPhaseSet = false;
private List samples = new ArrayList();
private int phaseSetId = 0;
private Map phaseSetIds = new HashMap();
@Override
public void header(final VcfHeader header) {
VcfHeaderLines headerLines = VcfHeaderLines.fromHeader(header);
if (headerLines.getFormatHeaderLines().containsKey("PS") &&
VcfHeaderLineType.String.equals(headerLines.getFormatHeaderLines().get("PS").getType())) {
remapPhaseSet = true;
VcfHeader.Builder builder = VcfHeader.builder().withFileFormat(header.getFileFormat());
for (String meta : header.getMeta()) {
if (meta.startsWith("##FORMAT=");
}
else {
builder.withMeta(meta);
}
}
VcfWriter.writeHeader(builder.build(), w);
}
else {
VcfWriter.writeHeader(header, w);
}
}
@Override
public void sample(final VcfSample sample) {
samples.add(sample);
}
@Override
public void record(final VcfRecord record) {
// write out samples
if (!wroteSamples) {
VcfWriter.writeColumnHeader(samples, w);
wroteSamples = true;
}
// write out record, remapping phase set if necessary
if (remapPhaseSet) {
Map genotypes = new HashMap(record.getGenotypes().size());
for (Map.Entry entry : record.getGenotypes().entrySet()) {
String sampleId = entry.getKey();
VcfGenotype genotype = entry.getValue();
if (genotype.containsFieldKey("PS")) {
String oldPhaseSetId = genotype.getFieldString("PS");
if (!phaseSetIds.containsKey(oldPhaseSetId)) {
phaseSetIds.put(oldPhaseSetId, phaseSetId);
phaseSetId++;
}
Integer newPhaseSetId = phaseSetIds.get(oldPhaseSetId);
genotypes.put(sampleId, VcfGenotype.builder(genotype).replaceField("PS", newPhaseSetId.toString()).build());
}
else {
genotypes.put(sampleId, genotype);
}
}
VcfWriter.writeRecord(samples, VcfRecord.builder(record).replaceGenotypes(genotypes).build(), w);
}
else {
VcfWriter.writeRecord(samples, record, w);
}
}
});
return 0;
}
finally {
try {
writer.close();
}
catch (Exception e) {
// empty
}
}
}
/**
* 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 inputVcfPath = new PathArgument("i", "input-vcf-path", "input VCF path, default stdin", false);
FileArgument outputVcfFile = new FileArgument("o", "output-vcf-file", "output VCF file, default stdout", false);
ArgumentList arguments = new ArgumentList(about, help, inputVcfPath, outputVcfFile);
CommandLine commandLine = new CommandLine(args);
RemapPhaseSet remapPhaseSet = 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);
}
remapPhaseSet = new RemapPhaseSet(inputVcfPath.getValue(), outputVcfFile.getValue());
}
catch (CommandLineParseException e) {
if (about.wasFound()) {
About.about(System.out);
System.exit(0);
}
if (help.wasFound()) {
Usage.usage(USAGE, null, commandLine, arguments, System.out);
System.exit(0);
}
Usage.usage(USAGE, e, commandLine, arguments, System.err);
System.exit(-1);
}
catch (NullPointerException | IllegalArgumentException e) {
Usage.usage(USAGE, e, commandLine, arguments, System.err);
System.exit(-1);
}
try {
System.exit(remapPhaseSet.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}
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