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/*
* The MIT License
*
* Copyright (c) 2014 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 picard.vcf;
import htsjdk.samtools.util.CollectionUtil;
import htsjdk.samtools.util.IOUtil;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.writer.Options;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
import htsjdk.variant.vcf.VCFFileReader;
import htsjdk.variant.vcf.VCFHeader;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.help.DocumentedFeature;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.StandardOptionDefinitions;
import picard.cmdline.programgroups.VariantManipulationProgramGroup;
import java.io.File;
import java.util.EnumSet;
/**
* Renames a sample within a VCF or BCF.
*
*
Summary
* This tool enables the user to rename a sample in either a VCF or BCF file. It is intended to change the name of a
* sample in a VCF prior to merging with VCF files in which one or more samples have similar names. Note that the
* input VCF file must be single-sample VCF and that the NEW_SAMPLE_NAME argument is required.
*
*
*
Inputs
*
*
Input single-sample VCF or BCF file.
*
Output single-sample VCF or BCF file.
*
New name to give sample in output VCF.
*
[Optional] Existing name of sample in VCF; if provided, asserts that that is the name of the extant sample name.
* The input VCF (or BCF) must be single-sample.
*
*/
@CommandLineProgramProperties(
summary = RenameSampleInVcf.USAGE_DETAILS,
oneLineSummary = RenameSampleInVcf.USAGE_SUMMARY,
programGroup = VariantManipulationProgramGroup.class)
@DocumentedFeature
public class RenameSampleInVcf extends CommandLineProgram {
static final String USAGE_SUMMARY = "Renames a sample within a VCF or BCF.";
static final String USAGE_DETAILS = "This tool enables the user to rename a sample in either a VCF or BCF file. " +
"It is intended to change the name of a sample in a VCF prior to merging with VCF files in which one or more samples have " +
"similar names. Note that the input VCF file must be single-sample VCF and that the NEW_SAMPLE_NAME is required." +
"
" +
" " +
"The input VCF (or BCF) must be single-sample.";
@Argument(shortName=StandardOptionDefinitions.INPUT_SHORT_NAME, doc="Input single sample VCF or BCF file.")
public File INPUT;
@Argument(shortName=StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc="Output single sample VCF.")
public File OUTPUT;
@Argument(doc="Existing name of sample in VCF; if provided, asserts that that is the name of the extant sample name", optional = true)
public String OLD_SAMPLE_NAME = null;
@Argument(doc="New name to give sample in output VCF.")
public String NEW_SAMPLE_NAME;
@Override
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsWritable(OUTPUT);
final VCFFileReader in = new VCFFileReader(INPUT, false);
final VCFHeader header = in.getFileHeader();
if (header.getGenotypeSamples().size() > 1) {
throw new IllegalArgumentException("Input VCF must be single-sample.");
}
if (OLD_SAMPLE_NAME != null && !OLD_SAMPLE_NAME.equals(header.getGenotypeSamples().get(0))) {
throw new IllegalArgumentException("Input VCF did not contain expected sample. Contained: " + header.getGenotypeSamples().get(0));
}
final EnumSet options = EnumSet.copyOf(VariantContextWriterBuilder.DEFAULT_OPTIONS);
if (CREATE_INDEX) options.add(Options.INDEX_ON_THE_FLY); else options.remove(Options.INDEX_ON_THE_FLY);
final VCFHeader outHeader = new VCFHeader(header.getMetaDataInInputOrder(), CollectionUtil.makeList(NEW_SAMPLE_NAME));
final VariantContextWriter out = new VariantContextWriterBuilder()
.setOptions(options)
.setOutputFile(OUTPUT).setReferenceDictionary(outHeader.getSequenceDictionary()).build();
out.writeHeader(outHeader);
for (final VariantContext ctx : in) {
out.add(ctx);
}
out.close();
in.close();
return 0;
}
}
