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Merge pull request #1206 from broadinstitute/eb_suppress_alt_allele_warnings 

Suppress emission of the scary warning message from genotyping to no …
This commit is contained in:
Eric Banks 2015-11-05 16:12:50 -05:00
parent 448b575701 2cc7de4886
commit 975f8a8502
1 changed files with 26 additions and 16 deletions
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42
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalculator.java
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@ -64,6 +64,10 @@ import java.util.*;
abstract class ExactAFCalculator extends AFCalculator {
protected static final int HOM_REF_INDEX = 0; // AA likelihoods are always first
// useful so that we don't keep printing out the same warning message
protected static boolean printedWarning = false;
/**
* Sorts {@link ExactAFCalculator.LikelihoodSum} instances where those with higher likelihood are first.
*/
@ -152,23 +156,29 @@ abstract class ExactAFCalculator extends AFCalculator {
if (altAlleleReduction == 0)
return vc;
else if (altAlleleReduction != 0) {
logger.warn("this tool is currently set to genotype at most " + maximumAlternativeAlleles
+ " 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");
final List<Allele> alleles = new ArrayList<>(maximumAlternativeAlleles + 1);
alleles.add(vc.getReference());
alleles.addAll(reduceScopeAlleles(vc, defaultPloidy, maximumAlternativeAlleles));
final VariantContextBuilder builder = new VariantContextBuilder(vc);
builder.alleles(alleles);
builder.genotypes(reduceScopeGenotypes(vc, defaultPloidy, alleles));
if (altAlleleReduction < 0)
throw new IllegalStateException("unexpected: reduction increased the number of alt. alleles!: " + - altAlleleReduction + " " + vc + " " + builder.make());
return builder.make();
} else // if (altAlleleReduction < 0)
throw new IllegalStateException("unexpected: reduction increased the number of alt. alleles!: " + - altAlleleReduction + " " + vc);
String message = "this tool is currently set to genotype at most " + maximumAlternativeAlleles
+ " alternate alleles in a given context, but the context at " + vc.getContig() + ":" + vc.getStart()
+ " has " + (vc.getAlternateAlleles().size())
+ " alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument";
if ( !printedWarning ) {
printedWarning = true;
message += ". This warning message is output just once per run and further warnings will be suppressed unless the DEBUG logging level is used.";
logger.warn(message);
} else {
logger.debug(message);
}
final List<Allele> alleles = new ArrayList<>(maximumAlternativeAlleles + 1);
alleles.add(vc.getReference());
alleles.addAll(reduceScopeAlleles(vc, defaultPloidy, maximumAlternativeAlleles));
final VariantContextBuilder builder = new VariantContextBuilder(vc);
builder.alleles(alleles);
builder.genotypes(reduceScopeGenotypes(vc, defaultPloidy, alleles));
if (altAlleleReduction < 0)
throw new IllegalStateException("unexpected: reduction increased the number of alt. alleles!: " + - altAlleleReduction + " " + vc + " " + builder.make());
return builder.make();
}
/**