From 8d48bdc9ec6076aa410f1caeb0dec8b790876942 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 8 Apr 2009 02:00:41 +0000
Subject: [PATCH] it walks... the version committed actually counts snps only

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@328 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/MendelianInheritanceWalker.java   | 118 ++++++++++++++++++
 1 file changed, 118 insertions(+)
 create mode 100644 java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java
new file mode 100644
index 000000000..fde51845f
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java
@@ -0,0 +1,118 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.rodSAMPileup;
+import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
+import org.broadinstitute.sting.gatk.walkers.RefWalker;
+import org.broadinstitute.sting.playground.utils.TrioConcordanceRecord;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+
+public class MendelianInheritanceWalker  extends RefWalker<TrioConcordanceRecord, TrioConcordanceRecord> {
+
+	@Argument(fullName="conf_cutoff", shortName="X",required=true ) public Double CONF_CUTOFF;
+	
+	private static Logger logger = Logger.getLogger(MendelianInheritanceWalker.class);	
+	
+	
+	@Override
+	public TrioConcordanceRecord map(RefMetaDataTracker rodData, char ref, LocusContext context) {
+		
+		TrioConcordanceRecord t = new TrioConcordanceRecord();
+		
+//		String outLine = new String(context.getLocation() + " REF: "+ref + " RODS:" + rodData.getAllRods().size());
+		
+		AllelicVariant mom = (rodSAMPileup)rodData.lookup("mother", null);
+		AllelicVariant dad = (rodSAMPileup)rodData.lookup("father", null);
+		AllelicVariant kid = (rodSAMPileup)rodData.lookup("daughter", null);
+		
+		if ( ! hasCall(mom)  || ! hasCall(dad) || ! hasCall(kid) ) return t; // at least one person is not called; nothing to do, bail out
+			
+		// proceed only if we got confident calls
+			
+        t.assessed_loci = 1;
+			
+		if ( ! mom.isBiallelic() || ! dad.isBiallelic() || ! kid.isBiallelic() ) {
+			t.non_biallelic = 1; // we currently ignore non-biallelic sites
+			return t;
+		}
+		
+		// ok, we got a call and it is biallelic (at most)
+		
+		if ( mom.isReference() && dad.isReference() && kid.isReference() ) { // got all refs, we are done
+			t.consistent_ref = 1;
+			return t;
+		}
+
+		// by now we know that there's a SNP
+		
+		String kid_allele_1 = kid.getGenotype().get(0);
+		String kid_allele_2 = kid.getGenotype().get(1);
+		List<String> mom_alleles = mom.getGenotype();
+		List<String> dad_alleles = dad.getGenotype();
+		
+		// kid must have one allele from mom and one allele from dad if it's not X chromosome!
+		
+		if ( mom_alleles.contains(kid_allele_1) && dad_alleles.contains(kid_allele_2) ||
+				mom_alleles.contains(kid_allele_2) && dad_alleles.contains(kid_allele_1) ) {
+			t.consistent_snp = 1;
+			
+			logger.info("consistent SNP at "+context.getLocation() + 
+					"("+ref+") " + mom_alleles.get(0)+"/" +mom_alleles.get(1) + "  " +
+					dad_alleles.get(0)+"/" +dad_alleles.get(1) + "  " +
+					kid_allele_1+"/" +kid_allele_2  
+					);
+			return t;
+	    }
+		
+		// snp is inconsistent
+		
+		t.inconsistent_snp = 1;
+		logger.info("INconsistent SNP at "+context.getLocation() + 
+				"("+ref+") " + mom_alleles.get(0)+"/" +mom_alleles.get(1) + "  " +
+				dad_alleles.get(0)+"/" +dad_alleles.get(1) + "  " +
+				kid_allele_1+"/" +kid_allele_2  
+				);
+		
+		return t;
+		
+	}
+
+	@Override
+	public TrioConcordanceRecord reduce(TrioConcordanceRecord value, TrioConcordanceRecord sum) {
+		
+		return sum.add(value);
+	}
+
+	@Override
+	public TrioConcordanceRecord reduceInit() {
+		
+		return new TrioConcordanceRecord();
+	}
+
+	boolean hasCall(AllelicVariant av) {
+		if ( av == null ) return false; // there's no call if there's no rod data available, duh!
+		if ( av.isReference() ) return av.getConsensusConfidence() >= CONF_CUTOFF ;
+		else return av.getVariationConfidence() >= CONF_CUTOFF;
+		
+	}
+	
+	protected String shortLine(AllelicVariant av) {
+		
+		if ( av == null )  return new String( "<NULL>");
+		
+		if ( av.isReference() ) return new String ("*");
+		
+		if ( av.isSNP() ) return av.getAltBasesFWD();
+		if ( av.isInsertion() ) return new String('+'+av.getAltBasesFWD());
+		if ( av.isDeletion() ) return new String('-'+av.getRefBasesFWD());
+		if ( av.isIndel() ) return new String('?'+av.getAltBasesFWD());
+		return new String("<missing data!!!>");
+	}
+	
+}