auxiliary class, a simple struct to keep together info like numbers of covered, assessed, ref/variant bases across the sample

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@769 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/utils/GenotypingCallStats.java

@@ -0,0 +1,47 @@
+package org.broadinstitute.sting.playground.utils;
+
+import org.broadinstitute.sting.utils.Utils;
+
+/**
+ * This class is a trivial wrapper for keeping together and passing around a few simple statistics relevant for genotyping:
+ * e.g. number of covered bases (have any observation at all), number of "assessed" bases (e.g. those with confidence level
+ * above some cutoff, so that a call was actually made), number of ref/variant calls etc.
+ * @author asivache
+ *
+ */
+public class GenotypingCallStats {
+	public long covered = 0; // number of loci covered in all 3 individuals (not necessarily confidently called)
+	public long assessed = 0; // number of loci with all 3 genotypes available at or above the specified cutoff
+	public long ref = 0; // number of assessed loci, where all 3 people have homogeneous reference allele
+	public int variant = 0; // number of assessed loci where a variant is observed in the individual
+	public int consistent_variant = 0; // variants that are consistent in any (application-specific) sense, e.g. variant matches variants in other members of the family trio
+	public int consistent_ref = 0; // reference calls that are consistent in any (app-specific) sense, e.g. consistent with other members of the family trio
+	public int non_biallelic_variant = 0; // number of variant calls that are not biallelic
+	
+	public GenotypingCallStats add(GenotypingCallStats other) {
+		this.covered += other.covered;
+		this.assessed += other.assessed;
+		this.ref += other.ref;
+		this.variant += other.variant;
+		this.consistent_variant += other.consistent_variant;
+		this.consistent_ref += other.consistent_ref;
+		this.non_biallelic_variant += other.non_biallelic_variant;
+		return this;
+	}
+	
+//	public int totalVariants() { return consistent_variant + inconsistent_variant + non_biallelic_variant; }
+	
+	public String toString() {
+		StringBuilder b = new StringBuilder();
+		
+		
+		b.append( String.format("      covered: %d%n      assessed: %d (%3.2f%%)%n         ref: %d (%3.2f%%)%n         variants: %d (%3.2f%%)%n            multiallelic: %d (%3.2f%%)%n", 
+				covered, assessed, Utils.percentage(assessed, covered), 
+				ref, Utils.percentage(ref,assessed),
+				variant, Utils.percentage(variant,assessed),
+				non_biallelic_variant, Utils.percentage(non_biallelic_variant, variant))
+			);
+		
+		return b.toString();
+	}
+}