139 lines
6.1 KiB
Java
Executable File
139 lines
6.1 KiB
Java
Executable File
/*
|
|
* Copyright (c) 2010 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 org.broadinstitute.sting.oneoffprojects.walkers.vcftools;
|
|
|
|
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
|
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
|
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
|
|
import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
|
|
import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
|
|
import org.broadinstitute.sting.gatk.refdata.*;
|
|
import org.broadinstitute.sting.gatk.walkers.RodWalker;
|
|
import org.broadinstitute.sting.gatk.walkers.Requires;
|
|
import org.broadinstitute.sting.gatk.walkers.DataSource;
|
|
import org.broadinstitute.sting.gatk.walkers.RMD;
|
|
import org.broadinstitute.sting.utils.*;
|
|
import org.broadinstitute.sting.commandline.Argument;
|
|
import org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator;
|
|
|
|
import java.util.EnumSet;
|
|
import java.util.Arrays;
|
|
|
|
/**
|
|
* Test routine for new VariantContext object
|
|
*/
|
|
@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="variants",type=ReferenceOrderedDatum.class)})
|
|
public class VCFToBeagleWalker extends RodWalker<Integer, VCFToBeagleWalker.Result> {
|
|
@Argument(shortName="trio", doc="If provide, treats the input VCF as a single record containing genotypes for a single trio; String formatted as dad+mom=child", required=false)
|
|
protected String TRIO_STRUCTURE;
|
|
|
|
private MendelianViolationEvaluator.TrioStructure trio = null;
|
|
|
|
public class Result {
|
|
int nVariants, nConverted;
|
|
}
|
|
|
|
public void initialize() {
|
|
if ( TRIO_STRUCTURE != null ) {
|
|
trio = MendelianViolationEvaluator.parseTrioDescription(TRIO_STRUCTURE);
|
|
out.printf("I id %s%n", Utils.join(" ", Arrays.asList(trio.mom, trio.mom, trio.dad, trio.dad, trio.child, trio.child)));
|
|
}
|
|
}
|
|
|
|
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
|
if ( ref != null ) {
|
|
EnumSet<VariantContext.Type> allowedTypes = EnumSet.of(VariantContext.Type.SNP);
|
|
|
|
VariantContext vc = tracker.getVariantContext(ref, "variants", allowedTypes, context.getLocation(), false);
|
|
|
|
if ( vc != null && vc.isBiallelic() && vc.isNotFiltered() ) {
|
|
if ( trio != null ) { // we are emitting a trio file
|
|
if ( ! vc.hasGenotypes() || vc.getGenotypes().size() != 3 )
|
|
throw new StingException("Convertion exception: Trio conversion requires exactly three genotypes at every locus: " + vc);
|
|
|
|
if ( genotypesAreGood(vc) ) {
|
|
if ( ! genotypesAreGoodForTrios(vc, trio) ) {
|
|
logger.debug("VC excluded due to poor trio genotyping " + vc);
|
|
} else {
|
|
Genotype mom = vc.getGenotype(trio.mom);
|
|
Genotype dad = vc.getGenotype(trio.dad);
|
|
Genotype child = vc.getGenotype(trio.child);
|
|
|
|
// beagle format looks like:
|
|
//
|
|
// I id 1001 1001 1002 1002 1003 1003
|
|
// A diabetes 1 1 2 2 2 2
|
|
// M rs2289311 A G G G A G
|
|
String loc = "c" + vc.getLocation().getContig() + "_p" + vc.getLocation().getStart();
|
|
out.printf("M %s %s %s %s%n", loc, genotype2BeagleString(mom), genotype2BeagleString(dad), genotype2BeagleString(child));
|
|
return 1;
|
|
}
|
|
}
|
|
} else {
|
|
throw new IllegalArgumentException("VCFToBeagle currently only supports conversion of trios. Complain to mark");
|
|
}
|
|
}
|
|
}
|
|
|
|
return 0;
|
|
}
|
|
|
|
private String genotype2BeagleString(Genotype g) {
|
|
return allele2BeagleString(g.getAllele(0)) + " " + allele2BeagleString(g.getAllele(1));
|
|
}
|
|
|
|
private String allele2BeagleString(Allele a) {
|
|
return new String(a.getBases());
|
|
}
|
|
|
|
private static boolean genotypesAreGood(VariantContext vc) {
|
|
for ( Genotype g : vc.getGenotypes().values() ) {
|
|
if ( g.isFiltered() )
|
|
return false;
|
|
}
|
|
|
|
return true;
|
|
}
|
|
|
|
private static boolean genotypesAreGoodForTrios(VariantContext vc, MendelianViolationEvaluator.TrioStructure trio) {
|
|
return ! MendelianViolationEvaluator.isViolation(vc, vc.getGenotype(trio.mom), vc.getGenotype(trio.dad), vc.getGenotype(trio.child));
|
|
}
|
|
|
|
public Result reduceInit() {
|
|
return new Result();
|
|
}
|
|
|
|
public Result reduce(Integer point, Result sum) {
|
|
sum.nVariants++;
|
|
sum.nConverted += point;
|
|
return sum;
|
|
}
|
|
|
|
public void onTraversalDone(Result result) {
|
|
logger.info(String.format("Saw %d raw SNPs", result.nVariants));
|
|
logger.info(String.format("Converted %d (%.2f%%) of these sites", result.nConverted, (100.0 * result.nConverted) / result.nVariants));
|
|
}
|
|
} |