From ddf87e61c2efc0739bb47ee9085518c74cfe59d9 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 29 Jun 2010 12:57:28 +0000
Subject: [PATCH] For Sendu: optionally emit a metrics file with callability
 info (including number of actual calls made) from UG

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3667 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/genotyper/UnifiedGenotyper.java   | 22 ++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 8ce3e9ab8..1fc81e759 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -57,6 +57,9 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
     @Argument(fullName = "verbose_mode", shortName = "verbose", doc = "File to print all of the annotated and detailed debugging output", required = false)
     public PrintStream verboseWriter = null;
 
+    @Argument(fullName = "metrics_file", shortName = "metrics", doc = "File to print any relevant callability metrics output", required = false)
+    public PrintStream metricsWriter = null;
+
     @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
     protected String[] annotationsToUse = {};
 
@@ -88,6 +91,9 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         /** The number of bases called confidently (according to user threshold), either ref or other */
         long nBasesCalledConfidently = 0;
 
+        /** The number of bases for which calls were emitted */
+        long nCallsMade = 0;
+
         /** The total number of extended events encountered */
         long nExtendedEvents = 0;
 
@@ -178,6 +184,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         lhs.nBasesCallable += rhs.nBasesCallable;
         lhs.nBasesCalledConfidently += rhs.nBasesCalledConfidently;
         lhs.nBasesVisited += rhs.nBasesVisited;
+        lhs.nCallsMade += rhs.nCallsMade;
         return lhs;
     }
 
@@ -192,7 +199,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         // A call was attempted -- the base was potentially callable
         sum.nBasesCallable++;
 
-        // if the base was confidently called something, print it out
+        // the base was confidently callable
         sum.nBasesCalledConfidently += value.confidentlyCalled ? 1 : 0;
 
         // can't make a confident variant call here
@@ -200,6 +207,8 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
             return sum;
 
         try {
+            // we are actually making a call
+            sum.nCallsMade++;
             writer.addCall(value.vc, value.refAllele);
         } catch (IllegalArgumentException e) {
             throw new IllegalArgumentException(e.getMessage() + "; this is often caused by using the --assume_single_sample_reads argument with the wrong sample name");
@@ -215,5 +224,16 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         logger.info(String.format("%% callable bases of all loci                 %3.3f", sum.percentCallableOfAll()));
         logger.info(String.format("%% confidently called bases of all loci       %3.3f", sum.percentCalledOfAll()));
         logger.info(String.format("%% confidently called bases of callable loci  %3.3f", sum.percentCalledOfCallable()));
+        logger.info(String.format("Actual calls made                            %d", sum.nCallsMade));
+
+        if ( metricsWriter != null ) {
+            metricsWriter.println(String.format("Visited bases                                %d", sum.nBasesVisited));
+            metricsWriter.println(String.format("Callable bases                               %d", sum.nBasesCallable));
+            metricsWriter.println(String.format("Confidently called bases                     %d", sum.nBasesCalledConfidently));
+            metricsWriter.println(String.format("%% callable bases of all loci                 %3.3f", sum.percentCallableOfAll()));
+            metricsWriter.println(String.format("%% confidently called bases of all loci       %3.3f", sum.percentCalledOfAll()));
+            metricsWriter.println(String.format("%% confidently called bases of callable loci  %3.3f", sum.percentCalledOfCallable()));
+            metricsWriter.println(String.format("Actual calls made                            %d", sum.nCallsMade));
+        }
     }
 }