From 5296de8251ddb1cd9036bf9b7e57fc362a78f92b Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sun, 21 Oct 2012 08:20:39 -0400 Subject: [PATCH] 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() --- .../genotyper/UnifiedArgumentCollection.java | 32 +++++++++++++------ 1 file changed, 22 insertions(+), 10 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index abf0b4420..e50f25fe8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -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; }