/*
* 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.SAMSequenceDictionary;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.ProgressLogger;
import htsjdk.variant.utils.SAMSequenceDictionaryExtractor;
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 picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.StandardOptionDefinitions;
import picard.cmdline.programgroups.VcfOrBcf;
import java.io.File;
/**
* Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.
*
* @author George Grant
*
*/
@CommandLineProgramProperties(
usage = "Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.",
usageShort = "Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.",
programGroup = VcfOrBcf.class
)
public class UpdateVcfSequenceDictionary extends CommandLineProgram {
@Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "Input VCF")
public File INPUT;
@Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "Output VCF to be written.")
public File OUTPUT;
@Option(shortName = StandardOptionDefinitions.SEQUENCE_DICTIONARY_SHORT_NAME, doc = "A Sequence Dictionary (can be read from one of the " +
"following file types (SAM, BAM, VCF, BCF, Interval List, Fasta, or Dict)")
public File SEQUENCE_DICTIONARY;
private final Log log = Log.getInstance(UpdateVcfSequenceDictionary.class);
public static void main(final String[] args) {
new UpdateVcfSequenceDictionary().instanceMainWithExit(args);
}
@Override
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsReadable(SEQUENCE_DICTIONARY);
IOUtil.assertFileIsWritable(OUTPUT);
final SAMSequenceDictionary samSequenceDictionary = SAMSequenceDictionaryExtractor.extractDictionary(SEQUENCE_DICTIONARY);
final VCFFileReader fileReader = new VCFFileReader(INPUT, false);
final VCFHeader fileHeader = fileReader.getFileHeader();
final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
.setReferenceDictionary(samSequenceDictionary)
.clearOptions();
if (CREATE_INDEX)
builder.setOption(Options.INDEX_ON_THE_FLY);
final VariantContextWriter vcfWriter = builder.setOutputFile(OUTPUT).build();
fileHeader.setSequenceDictionary(samSequenceDictionary);
vcfWriter.writeHeader(fileHeader);
final ProgressLogger progress = new ProgressLogger(log, 10000);
final CloseableIterator<VariantContext> iterator = fileReader.iterator();
while (iterator.hasNext()) {
final VariantContext context = iterator.next();
vcfWriter.add(context);
progress.record(context.getChr(), context.getStart());
}
CloserUtil.close(iterator);
CloserUtil.close(fileReader);
vcfWriter.close();
return 0;
}
}