From 119ca7d742371423060bcc7150f908e1cb04de8a Mon Sep 17 00:00:00 2001
From: Laurent Francioli <lfran@broadinstitute.org>
Date: Wed, 2 Nov 2011 08:22:33 +0100
Subject: [PATCH] Fixed a bug in parent/child pairs reporting causing a crash
 in case the -mvf option was used and mother was not provided

---
 .../sting/gatk/walkers/phasing/PhaseByTransmission.java  | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
index 5b2024f96..806a84e9d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
@@ -681,6 +681,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
         metricsCounters.put(NUM_PAIR_GENOTYPES_PHASED,0);
         metricsCounters.put(NUM_PAIR_HET_HET,0);
         metricsCounters.put(NUM_PAIR_VIOLATIONS,0);
+        String mvfLine = "";
 
         if (tracker != null) {
             VariantContext vc = tracker.getFirstValue(variantCollection.variants, context.getLocation());
@@ -712,19 +713,23 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
                     if(father != null){
                         genotypeMap.put(phasedFather.getSampleName(), phasedFather);
                         updateTrioMetricsCounters(phasedMother,phasedFather,phasedChild,isMV,metricsCounters);
+                        mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t%s:%s:%s:%s\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getAttribute(VCFConstants.DEPTH_KEY),phasedMother.getAttribute("AD"),phasedMother.getLikelihoods().toString(),phasedFather.getGenotypeString(),phasedFather.getAttribute(VCFConstants.DEPTH_KEY),phasedFather.getAttribute("AD"),phasedFather.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString());
                     }
-                    else
+                    else{
                         updatePairMetricsCounters(phasedMother,phasedChild,isMV,metricsCounters);
+                        mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t.:.:.:.\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getAttribute(VCFConstants.DEPTH_KEY),phasedMother.getAttribute("AD"),phasedMother.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString());
+                    }
                 }
                 else{
                     genotypeMap.put(phasedFather.getSampleName(),phasedFather);
                     updatePairMetricsCounters(phasedFather,phasedChild,isMV,metricsCounters);
+                    mvfLine =   String.format("%s\t%d\t%s\t%s\t%s\t%s\t.:.:.:.\t%s:%s:%s:%s\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedFather.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedFather.getGenotypeString(),phasedFather.getAttribute(VCFConstants.DEPTH_KEY),phasedFather.getAttribute("AD"),phasedFather.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString());
                     }
 
                 //Report violation if set so
                 //TODO: ADAPT FOR PAIRS TOO!!
                 if(isMV && mvFile != null)
-                    mvFile.println(String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t%s:%s:%s:%s\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getAttribute(VCFConstants.DEPTH_KEY),phasedMother.getAttribute("AD"),phasedMother.getLikelihoods().toString(),phasedFather.getGenotypeString(),phasedFather.getAttribute(VCFConstants.DEPTH_KEY),phasedFather.getAttribute("AD"),phasedFather.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString()));
+                    mvFile.println(mvfLine);
 
             }