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deprecate -stand_emit_conf

This commit is contained in:
Ron Levine 2016-10-02 12:13:18 -04:00
parent 7b3af3820e
commit 81a9ece45b
1 changed files with 10 additions and 0 deletions
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10
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java
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@ -54,6 +54,7 @@ package org.broadinstitute.gatk.engine.arguments;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculator; import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculator;
import org.broadinstitute.gatk.utils.commandline.Advanced; import org.broadinstitute.gatk.utils.commandline.Advanced;
import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.Hidden;
import org.broadinstitute.gatk.utils.variant.HomoSapiensConstants; import org.broadinstitute.gatk.utils.variant.HomoSapiensConstants;
import java.util.Collections; import java.util.Collections;
@ -123,6 +124,15 @@ public class GenotypeCalculationArgumentCollection implements Cloneable{
@Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be called", required = false) @Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be called", required = false)
public double STANDARD_CONFIDENCE_FOR_CALLING = 30.0; public double STANDARD_CONFIDENCE_FOR_CALLING = 30.0;
/**
* This argument allows you to emit low quality calls as filtered records.
*/
@Hidden
@Deprecated
@Argument(fullName = "standard_min_confidence_threshold_for_emitting", shortName = "stand_emit_conf",
doc = "This argument is no longer used in GATK versions 3.7 and newer. Please see the online documentation for the latest usage recommendations.", required = false)
public double STANDARD_CONFIDENCE_FOR_EMITTING = 30.0;
/** /**
* 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 and it * then only this many alleles will be used. Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it