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Support for selecting only variants with specific IDs from a file in SelectVariants 

-- Cleaned up unused variables as well
This commit is contained in:
Mark DePristo 2011-12-16 16:10:18 -05:00
parent d6d2f49c88
commit b6067be952
1 changed files with 47 additions and 40 deletions
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87
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.MendelianViolation; import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
@ -42,6 +43,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import java.io.File; import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.*; import java.util.*;
@ -140,7 +142,7 @@ import java.util.*;
* -R ref.fasta \ * -R ref.fasta \
* -T SelectVariants \ * -T SelectVariants \
* --variant input.vcf \ * --variant input.vcf \
* -family NA12891+NA12892=NA12878 \ * -bed family.ped \
* -mvq 50 \ * -mvq 50 \
* -o violations.vcf * -o violations.vcf
* *
@ -250,16 +252,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
@Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't update the AC, AF, or AN values in the INFO field after selecting", required=false) @Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't update the AC, AF, or AN values in the INFO field after selecting", required=false)
private boolean KEEP_ORIGINAL_CHR_COUNTS = false; private boolean KEEP_ORIGINAL_CHR_COUNTS = false;
@Hidden
@Argument(fullName="family_structure_file", shortName="familyFile", doc="use -family unless you know what you're doing", required=false)
private File FAMILY_STRUCTURE_FILE = null;
/**
* String formatted as dad+mom=child where these parameters determine which sample names are examined.
*/
@Argument(fullName="family_structure", shortName="family", doc="string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false)
private String FAMILY_STRUCTURE = "";
/** /**
* This activates the mendelian violation module that will select all variants that correspond to a mendelian violation following the rules given by the family structure. * This activates the mendelian violation module that will select all variants that correspond to a mendelian violation following the rules given by the family structure.
*/ */
@ -286,13 +278,21 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
private double fractionGenotypes = 0; private double fractionGenotypes = 0;
/** /**
* This argument select particular kinds of variants out of a list. If left empty, there is no type selection and all variant types are considered for other selection criteria. * This argument select particular kinds of variants out of a list. If left empty, there is no type selection and all variant types are considered for other selection criteria.
* When specified one or more times, a particular type of variant is selected. * When specified one or more times, a particular type of variant is selected.
* *
*/ */
@Argument(fullName="selectTypeToInclude", shortName="selectType", doc="Select only a certain type of variants from the input file. Valid types are INDEL, SNP, MIXED, MNP, SYMBOLIC, NO_VARIATION. Can be specified multiple times", required=false) @Argument(fullName="selectTypeToInclude", shortName="selectType", doc="Select only a certain type of variants from the input file. Valid types are INDEL, SNP, MIXED, MNP, SYMBOLIC, NO_VARIATION. Can be specified multiple times", required=false)
private List<VariantContext.Type> TYPES_TO_INCLUDE = new ArrayList<VariantContext.Type>(); private List<VariantContext.Type> TYPES_TO_INCLUDE = new ArrayList<VariantContext.Type>();
/**
* If provided, we will only include variants whose ID field is present in this list of ids. The matching
* is exact string matching. The file format is just one ID per line
*
*/
@Argument(fullName="keepIDs", shortName="IDs", doc="Only emit sites whose ID is found in this file (one ID per line)", required=false)
private File rsIDFile = null;
@Hidden @Hidden
@Argument(fullName="outMVFile", shortName="outMVFile", doc="", required=false) @Argument(fullName="outMVFile", shortName="outMVFile", doc="", required=false)
@ -313,9 +313,9 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
} }
public enum NumberAlleleRestriction { public enum NumberAlleleRestriction {
ALL, ALL,
BIALLELIC, BIALLELIC,
MULTIALLELIC MULTIALLELIC
} }
private ArrayList<VariantContext.Type> selectedTypes = new ArrayList<VariantContext.Type>(); private ArrayList<VariantContext.Type> selectedTypes = new ArrayList<VariantContext.Type>();
@ -339,17 +339,13 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
private int positionToAdd = 0; private int positionToAdd = 0;
private RandomVariantStructure [] variantArray; private RandomVariantStructure [] variantArray;
/* Variables used for random selection with AF boosting */
private ArrayList<Double> afBreakpoints = null;
private ArrayList<Double> afBoosts = null;
double bkDelta = 0.0;
private PrintStream outMVFileStream = null; private PrintStream outMVFileStream = null;
//Random number generator for the genotypes to remove //Random number generator for the genotypes to remove
private Random randomGenotypes = new Random(); private Random randomGenotypes = new Random();
private Set<String> IDsToKeep = null;
/** /**
* Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher * Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher
*/ */
@ -437,7 +433,18 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
if (SELECT_RANDOM_FRACTION) logger.info("Selecting approximately " + 100.0*fractionRandom + "% of the variants at random from the variant track"); if (SELECT_RANDOM_FRACTION) logger.info("Selecting approximately " + 100.0*fractionRandom + "% of the variants at random from the variant track");
/** load in the IDs file to a hashset for matching */
if ( rsIDFile != null ) {
IDsToKeep = new HashSet<String>();
try {
for ( final String line : new XReadLines(rsIDFile).readLines() ) {
IDsToKeep.add(line.trim());
}
logger.info("Selecting only variants with one of " + IDsToKeep.size() + " IDs from " + rsIDFile);
} catch ( FileNotFoundException e ) {
throw new UserException.CouldNotReadInputFile(rsIDFile, e);
}
}
} }
/** /**
@ -460,20 +467,23 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
} }
for (VariantContext vc : vcs) { for (VariantContext vc : vcs) {
if ( IDsToKeep != null && ! IDsToKeep.contains(vc.getID()) )
continue;
if (MENDELIAN_VIOLATIONS && mv.countViolations(this.getSampleDB().getFamilies(samples),vc) < 1) if (MENDELIAN_VIOLATIONS && mv.countViolations(this.getSampleDB().getFamilies(samples),vc) < 1)
break; break;
if (outMVFile != null){ if (outMVFile != null){
for( String familyId : mv.getViolationFamilies()){ for( String familyId : mv.getViolationFamilies()){
for(Sample sample : this.getSampleDB().getFamily(familyId)){ for(Sample sample : this.getSampleDB().getFamily(familyId)){
if(sample.getParents().size() > 0){ if(sample.getParents().size() > 0){
outMVFileStream.format("MV@%s:%d. REF=%s, ALT=%s, AC=%d, momID=%s, dadID=%s, childID=%s, momG=%s, momGL=%s, dadG=%s, dadGL=%s, " + outMVFileStream.format("MV@%s:%d. REF=%s, ALT=%s, AC=%d, momID=%s, dadID=%s, childID=%s, momG=%s, momGL=%s, dadG=%s, dadGL=%s, " +
"childG=%s childGL=%s\n",vc.getChr(), vc.getStart(), "childG=%s childGL=%s\n",vc.getChr(), vc.getStart(),
vc.getReference().getDisplayString(), vc.getAlternateAllele(0).getDisplayString(), vc.getCalledChrCount(vc.getAlternateAllele(0)), vc.getReference().getDisplayString(), vc.getAlternateAllele(0).getDisplayString(), vc.getCalledChrCount(vc.getAlternateAllele(0)),
sample.getMaternalID(), sample.getPaternalID(), sample.getID(), sample.getMaternalID(), sample.getPaternalID(), sample.getID(),
vc.getGenotype(sample.getMaternalID()).toBriefString(), vc.getGenotype(sample.getMaternalID()).getLikelihoods().getAsString(), vc.getGenotype(sample.getMaternalID()).toBriefString(), vc.getGenotype(sample.getMaternalID()).getLikelihoods().getAsString(),
vc.getGenotype(sample.getPaternalID()).toBriefString(), vc.getGenotype(sample.getPaternalID()).getLikelihoods().getAsString(), vc.getGenotype(sample.getPaternalID()).toBriefString(), vc.getGenotype(sample.getPaternalID()).getLikelihoods().getAsString(),
vc.getGenotype(sample.getID()).toBriefString(),vc.getGenotype(sample.getID()).getLikelihoods().getAsString() ); vc.getGenotype(sample.getID()).toBriefString(),vc.getGenotype(sample.getID()).getLikelihoods().getAsString() );
} }
} }
@ -513,10 +523,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
else if (!SELECT_RANDOM_FRACTION || ( GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) { else if (!SELECT_RANDOM_FRACTION || ( GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) {
vcfWriter.add(sub); vcfWriter.add(sub);
} }
} }
} }
return 1; return 1;
@ -647,7 +654,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
// if we have fewer alternate alleles in the selected VC than in the original VC, we need to strip out the GL/PLs (because they are no longer accurate) // if we have fewer alternate alleles in the selected VC than in the original VC, we need to strip out the GL/PLs (because they are no longer accurate)
if ( vc.getAlleles().size() != sub.getAlleles().size() ) if ( vc.getAlleles().size() != sub.getAlleles().size() )
newGC = VariantContextUtils.stripPLs(sub.getGenotypes()); newGC = VariantContextUtils.stripPLs(sub.getGenotypes());
//Remove a fraction of the genotypes if needed //Remove a fraction of the genotypes if needed
if(fractionGenotypes>0){ if(fractionGenotypes>0){
@ -655,10 +662,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
for ( Genotype genotype : newGC ) { for ( Genotype genotype : newGC ) {
//Set genotype to no call if it falls in the fraction. //Set genotype to no call if it falls in the fraction.
if(fractionGenotypes>0 && randomGenotypes.nextDouble()<fractionGenotypes){ if(fractionGenotypes>0 && randomGenotypes.nextDouble()<fractionGenotypes){
ArrayList<Allele> alleles = new ArrayList<Allele>(2); ArrayList<Allele> alleles = new ArrayList<Allele>(2);
alleles.add(Allele.create((byte)'.')); alleles.add(Allele.create((byte)'.'));
alleles.add(Allele.create((byte)'.')); alleles.add(Allele.create((byte)'.'));
genotypes.add(new Genotype(genotype.getSampleName(),alleles, Genotype.NO_LOG10_PERROR,genotype.getFilters(),new HashMap<String, Object>(),false)); genotypes.add(new Genotype(genotype.getSampleName(),alleles, Genotype.NO_LOG10_PERROR,genotype.getFilters(),new HashMap<String, Object>(),false));
} }
else{ else{
genotypes.add(genotype); genotypes.add(genotype);