/*
* 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 picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.StandardOptionDefinitions;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.CollectionUtil;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.writer.Options;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
import htsjdk.variant.vcf.VCFFileReader;
import htsjdk.variant.vcf.VCFHeader;
import picard.cmdline.programgroups.VcfOrBcf;
import java.io.File;
import java.util.EnumSet;
@CommandLineProgramProperties(
usage = "Rename a sample within a VCF or BCF.",
usageShort = "Rename a sample within a VCF or BCF.",
programGroup = VcfOrBcf.class
)
public class RenameSampleInVcf extends CommandLineProgram {
@Option(shortName=StandardOptionDefinitions.INPUT_SHORT_NAME, doc="Input single sample VCF.")
public File INPUT;
@Option(shortName=StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc="Output single sample VCF.")
public File OUTPUT;
@Option(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;
@Option(doc="New name to give sample in output VCF.")
public String NEW_SAMPLE_NAME;
public static void main(final String[] args) {
new RenameSampleInVcf().instanceMainWithExit(args);
}
@Override
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsWritable(OUTPUT);
final VCFFileReader in = new VCFFileReader(INPUT);
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> options = EnumSet.copyOf(VariantContextWriterFactory.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 = VariantContextWriterFactory.create(OUTPUT, outHeader.getSequenceDictionary(), options);
out.writeHeader(outHeader);
for (final VariantContext ctx : in) {
out.add(ctx);
}
out.close();
in.close();
return 0;
}
}