From fcc347bb05c0d3048a2fb51dd490fb443926b8ea Mon Sep 17 00:00:00 2001
From: carneiro <carneiro@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 14 Mar 2011 20:32:09 +0000
Subject: [PATCH] making sure the output is as pretty as I said it would be on
 the wiki.

wikipage for this walker is up, at : http://www.broadinstitute.org/gsa/wiki/index.php/Genotype_and_Validate#Examples

use it ;)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5442 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/GenotypeAndValidateWalker.java    | 27 ++++++++++---------
 1 file changed, 15 insertions(+), 12 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/GenotypeAndValidateWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/GenotypeAndValidateWalker.java
index f54c602c6..d8c71ebbc 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/GenotypeAndValidateWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/GenotypeAndValidateWalker.java
@@ -166,8 +166,10 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
             return counter;
 
         // Do not operate on variants that are not covered to the optional minimum depth
-        if (!context.hasReads() || minDepth > 0 && context.getBasePileup().getBases().length < minDepth) {
-            counter.numUncovered = 1L;
+        if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
+            // don't count indel extended events multiple times as uncovered.
+        //    if (vcComp.getStart() == ref.getLocus().getStart())                  //todo - not sure I want this, may be misleading to filter anything.
+                counter.numUncovered = 1L;
             return counter;
         }
 
@@ -179,15 +181,15 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
             call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
         else if ( vcComp.isIndel() ) {
             call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
-            if (call.vc == null) // variant context will be null on an extended indel event and I just want to call it one event.
-                return counter;
+//            if (call.vc == null) // variant context will be null on an extended indel event and I just want to call it one event.
+//                return counter;
         }
         else {
             logger.info("Not SNP or INDEL " + vcComp.getChr() + ":" + vcComp.getStart() + " " + vcComp.getAlleles());
             return counter;
         }
 
-        if (!call.confidentlyCalled) {
+        if (!call.confidentlyCalled) {                                           //todo - maybe filter extended indel events to count as one only if it's entirely successful?
             counter.numNotConfidentCalls = 1L;
             if (vcComp.getFilters().contains("TP"))
                 counter.numFN = 1L;
@@ -227,14 +229,15 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
     }
 
     public void onTraversalDone( CountedData reduceSum ) {
-        logger.info("TP = " + reduceSum.numTP);
-        logger.info("TN = " + reduceSum.numTN);
-        logger.info("FP = " + reduceSum.numFP);
-        logger.info("FN = " + reduceSum.numFN);
-        logger.info("PPV = " + ((double) reduceSum.numTP /( reduceSum.numTP + reduceSum.numFP)));
-        logger.info("NPV = " + ((double) reduceSum.numTN /( reduceSum.numTN + reduceSum.numFN)));
-        logger.info("Uncovered = " + reduceSum.numUncovered);
+        logger.info("(status / truth)");
+        logger.info("called / true      = " + reduceSum.numTP);
+        logger.info("not called / false = " + reduceSum.numTN);
+        logger.info("called /false      = " + reduceSum.numFP);
+        logger.info("not called / true = " + reduceSum.numFN);
+        logger.info("PPV = " + 100 * ((double) reduceSum.numTP /( reduceSum.numTP + reduceSum.numFP)) + "%");
+        logger.info("NPV = " + 100 * ((double) reduceSum.numTN /( reduceSum.numTN + reduceSum.numFN)) + "%");
         logger.info("confidently called = " + reduceSum.numConfidentCalls);
         logger.info("not confidently called = " + reduceSum.numNotConfidentCalls );
+        logger.info("Uncovered = " + reduceSum.numUncovered);
     }
 }