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Warn user when trying to run with EMIT_ALL_SITES with indels; better docs for that option.

This commit is contained in:
Eric Banks 2012-01-25 11:50:12 -05:00
parent e349b4b14b
commit fb863dc6a7
2 changed files with 9 additions and 2 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -205,6 +205,12 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
*
**/
public void initialize() {
// warn the user for misusing EMIT_ALL_SITES
if ( UAC.OutputMode == UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES &&
UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY &&
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");
// get all of the unique sample names
Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());

5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -54,8 +54,9 @@ public class UnifiedGenotyperEngine {
EMIT_VARIANTS_ONLY,
/** produces calls at variant sites and confident reference sites */
EMIT_ALL_CONFIDENT_SITES,
/** produces calls at any callable site regardless of confidence; this argument is intended for point
* mutations (SNPs) only and while some indel calls may be produced they are by no means comprehensive */
/** produces calls at any callable site regardless of confidence; this argument 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 */
EMIT_ALL_SITES
}