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Added @Hidden option for GSA production use to cap the max alleles for indels at a lower number than for SNPs

This commit is contained in:
Eric Banks 2012-05-21 16:03:29 -04:00
parent e57cd78bba
commit 666862af19
3 changed files with 14 additions and 7 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
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@ -52,17 +52,17 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
protected int N; protected int N;
protected int MAX_ALTERNATE_ALLELES_TO_GENOTYPE; protected int MAX_ALTERNATE_ALLELES_TO_GENOTYPE;
protected boolean CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS;
protected Logger logger; protected Logger logger;
protected PrintStream verboseWriter; protected PrintStream verboseWriter;
protected enum GenotypeType { AA, AB, BB }
protected static final double VALUE_NOT_CALCULATED = Double.NEGATIVE_INFINITY; protected static final double VALUE_NOT_CALCULATED = Double.NEGATIVE_INFINITY;
protected AlleleFrequencyCalculationModel(final UnifiedArgumentCollection UAC, final int N, final Logger logger, final PrintStream verboseWriter) { protected AlleleFrequencyCalculationModel(final UnifiedArgumentCollection UAC, final int N, final Logger logger, final PrintStream verboseWriter) {
this.N = N; this.N = N;
this.MAX_ALTERNATE_ALLELES_TO_GENOTYPE = UAC.MAX_ALTERNATE_ALLELES; this.MAX_ALTERNATE_ALLELES_TO_GENOTYPE = UAC.MAX_ALTERNATE_ALLELES;
this.CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS = UAC.CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS;
this.logger = logger; this.logger = logger;
this.verboseWriter = verboseWriter; this.verboseWriter = verboseWriter;
} }

12
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -49,13 +49,15 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
GenotypesContext GLs = vc.getGenotypes(); GenotypesContext GLs = vc.getGenotypes();
List<Allele> alleles = vc.getAlleles(); List<Allele> alleles = vc.getAlleles();
// don't try to genotype too many alternate alleles final int myMaxAltAllelesToGenotype = CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS && vc.getType().equals(VariantContext.Type.INDEL) ? 2 : MAX_ALTERNATE_ALLELES_TO_GENOTYPE;
if ( vc.getAlternateAlleles().size() > MAX_ALTERNATE_ALLELES_TO_GENOTYPE ) {
logger.warn("this tool is currently set to genotype at most " + MAX_ALTERNATE_ALLELES_TO_GENOTYPE + " alternate alleles in a given context, but the context at " + vc.getChr() + ":" + vc.getStart() + " has " + (vc.getAlternateAlleles().size()) + " alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument");
alleles = new ArrayList<Allele>(MAX_ALTERNATE_ALLELES_TO_GENOTYPE + 1); // don't try to genotype too many alternate alleles
if ( vc.getAlternateAlleles().size() > myMaxAltAllelesToGenotype ) {
logger.warn("this tool is currently set to genotype at most " + myMaxAltAllelesToGenotype + " alternate alleles in a given context, but the context at " + vc.getChr() + ":" + vc.getStart() + " has " + (vc.getAlternateAlleles().size()) + " alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument");
alleles = new ArrayList<Allele>(myMaxAltAllelesToGenotype + 1);
alleles.add(vc.getReference()); alleles.add(vc.getReference());
alleles.addAll(chooseMostLikelyAlternateAlleles(vc, MAX_ALTERNATE_ALLELES_TO_GENOTYPE)); alleles.addAll(chooseMostLikelyAlternateAlleles(vc, myMaxAltAllelesToGenotype));
GLs = VariantContextUtils.subsetDiploidAlleles(vc, alleles, false); GLs = VariantContextUtils.subsetDiploidAlleles(vc, alleles, false);
} }

5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -117,6 +117,10 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "max_alternate_alleles", shortName = "maxAlleles", doc = "Maximum number of alternate alleles to genotype", required = false) @Argument(fullName = "max_alternate_alleles", shortName = "maxAlleles", doc = "Maximum number of alternate alleles to genotype", required = false)
public int MAX_ALTERNATE_ALLELES = 3; public int MAX_ALTERNATE_ALLELES = 3;
@Hidden
@Argument(fullName = "cap_max_alternate_alleles_for_indels", shortName = "capMaxAllelesForIndels", doc = "Cap the maximum number of alternate alleles to genotype for indel calls at 2; overrides the --max_alternate_alleles argument; GSA production use only", required = false)
public boolean CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS = false;
// indel-related arguments // indel-related arguments
/** /**
* A candidate indel is genotyped (and potentially called) if there are this number of reads with a consensus indel at a site. * A candidate indel is genotyped (and potentially called) if there are this number of reads with a consensus indel at a site.
@ -192,6 +196,7 @@ public class UnifiedArgumentCollection {
uac.INDEL_HAPLOTYPE_SIZE = INDEL_HAPLOTYPE_SIZE; uac.INDEL_HAPLOTYPE_SIZE = INDEL_HAPLOTYPE_SIZE;
uac.alleles = alleles; uac.alleles = alleles;
uac.MAX_ALTERNATE_ALLELES = MAX_ALTERNATE_ALLELES; uac.MAX_ALTERNATE_ALLELES = MAX_ALTERNATE_ALLELES;
uac.CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS = CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS;
// todo- arguments to remove // todo- arguments to remove
uac.IGNORE_SNP_ALLELES = IGNORE_SNP_ALLELES; uac.IGNORE_SNP_ALLELES = IGNORE_SNP_ALLELES;