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Fix UnifiedArgumentCollection constructor logic error 

-- The old way of overloading constructors and calling super didn't work (might have been a consequence of merge).  This is the right way to do the copy constructor with the call to super()
This commit is contained in:
Mark DePristo 2012-10-21 08:20:39 -04:00
parent d21e42608a
commit 5296de8251
1 changed files with 22 additions and 10 deletions
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32
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -27,15 +27,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
<<<<<<< HEAD
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory;
import org.broadinstitute.sting.utils.pairhmm.PairHMM;
=======
>>>>>>> 19181ee... Moving pnrm to UnifiedArgumentCollection so it's available with the HaplotypeCaller
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
public class UnifiedArgumentCollection extends StandardCallerArgumentCollection {
@Argument(fullName = "genotype_likelihoods_model", shortName = "glm", doc = "Genotype likelihoods calculation model to employ -- SNP is the default option, while INDEL is also available for calling indels and BOTH is available for calling both together", required = false)
@ -182,14 +177,30 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
@Argument(shortName="ef", fullName="exclude_filtered_reference_sites", doc="Don't include in the analysis sites where the reference sample VCF is filtered. Default: false.", required=false)
boolean EXCLUDE_FILTERED_REFERENCE_SITES = false;
public UnifiedArgumentCollection() { }
public UnifiedArgumentCollection(final StandardCallerArgumentCollection SCAC) {
super(SCAC);
/**
* Create a new UAC with defaults for all UAC arguments
*/
public UnifiedArgumentCollection() {
super();
}
// Developers must remember to add any newly added arguments to the list here as well otherwise they won't get changed from their default value!
/**
* Create a new UAC based on the information only our in super-class scac and defaults for all UAC arguments
* @param scac
*/
public UnifiedArgumentCollection(final StandardCallerArgumentCollection scac) {
super(scac);
}
/**
* Create a new UAC with all parameters having the values in uac
*
* @param uac
*/
public UnifiedArgumentCollection(final UnifiedArgumentCollection uac) {
// Developers must remember to add any newly added arguments to the list here as well otherwise they won't get changed from their default value!
super(uac);
this.GLmodel = uac.GLmodel;
this.AFmodel = uac.AFmodel;
this.PCR_error = uac.PCR_error;
@ -215,6 +226,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
this.EXCLUDE_FILTERED_REFERENCE_SITES = uac.EXCLUDE_FILTERED_REFERENCE_SITES;
this.IGNORE_LANE_INFO = uac.IGNORE_LANE_INFO;
this.pairHMM = uac.pairHMM;
// todo- arguments to remove
this.IGNORE_SNP_ALLELES = uac.IGNORE_SNP_ALLELES;
}