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Minor tweak to the warning message.

This commit is contained in:
Eric Banks 2012-01-25 11:55:33 -05:00
parent fb863dc6a7
commit 96b62daff3
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -209,7 +209,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
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 &&
UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.SNP ) UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.SNP )
logger.warn("Note that the EMIT_ALL_SITES option is intended only for point mutations (SNPs) in DISCOVERY mode or generally when running in GENOTYPE_GIVEN_ALLELES mode; it will by no means produce a comprehensive set of indels in DISCOVERY mode"); logger.warn("WARNING: note that the EMIT_ALL_SITES option is intended only for point mutations (SNPs) in DISCOVERY mode or generally when running in GENOTYPE_GIVEN_ALLELES mode; it will by no means produce a comprehensive set of indels in DISCOVERY mode");
// get all of the unique sample names // get all of the unique sample names
Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()); Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());