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Don't allow users to try to genotype more than the max possible value (catch and throw a User Error at startup). Better docs explaining that users shouldn't play with this value unless they know what they are doing.

This commit is contained in:
Eric Banks 2012-04-12 09:18:44 -04:00
parent f46f7d0590
commit cc71baf691
3 changed files with 11 additions and 2 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -105,8 +105,11 @@ public class UnifiedArgumentCollection {
/** /**
* If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES), * If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES),
* then only this many alleles will be used. Note that genotyping sites with many alternate alleles is both CPU and memory intensive. * then only this many alleles will be used. Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it
* scales exponentially based on the number of alternate alleles. Unless there is a good reason to change the default value, we highly recommend
* that you not play around with this parameter.
*/ */
@Advanced
@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;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -39,6 +39,8 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.PrintStream; import java.io.PrintStream;
@ -207,6 +209,10 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
* *
**/ **/
public void initialize() { public void initialize() {
// check for a bad max alleles value
if ( UAC.MAX_ALTERNATE_ALLELES > GenotypeLikelihoods.MAX_ALLELES_THAT_CAN_BE_GENOTYPED )
throw new UserException.BadArgumentValue("max_alternate_alleles", "the maximum possible value is " + GenotypeLikelihoods.MAX_ALLELES_THAT_CAN_BE_GENOTYPED);
// warn the user for misusing EMIT_ALL_SITES // warn the user for misusing EMIT_ALL_SITES
if ( UAC.OutputMode == UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES && if ( UAC.OutputMode == UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES &&
UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY &&

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
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@ -223,7 +223,7 @@ public class GenotypeLikelihoods {
/** /**
* The maximum number of alleles that we can represent as genotype likelihoods * The maximum number of alleles that we can represent as genotype likelihoods
*/ */
final static int MAX_ALLELES_THAT_CAN_BE_GENOTYPED = 500; public final static int MAX_ALLELES_THAT_CAN_BE_GENOTYPED = 500;
/* /*
* a cache of the PL index to the 2 alleles it represents over all possible numbers of alternate alleles * a cache of the PL index to the 2 alleles it represents over all possible numbers of alternate alleles