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Suppress emission of the scary warning message from genotyping to no more than once in 

anything but DEBUG logging mode.  Otherwise it fills up our output logs.
This commit is contained in:
Eric Banks 2015-11-05 14:14:47 -05:00
parent 3d1dc303b3
commit 2cc7de4886
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();
}
/**