From 79bc878e6a9a280fd7873eca7b2861690dbf2628 Mon Sep 17 00:00:00 2001
From: Menachem Fromer <fromer@broadinstitute.org>
Date: Tue, 27 Nov 2012 22:37:41 -0500
Subject: [PATCH 3/3] Allow debugging to be set from the command line

---
 .../sting/gatk/walkers/phasing/ReadBackedPhasing.java    | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
index d8ae6b28b..eda43e6a5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
@@ -95,7 +95,8 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
 
 @DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
 public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
-    private static final boolean DEBUG = false;
+    @Argument(fullName="debug", shortName="debug", doc="If specified, print out very verbose debug information (if -l DEBUG is also specified)", required = false)
+    protected boolean DEBUG = false;
     /**
      * The VCF file we are phasing variants from.
      *
@@ -949,7 +950,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
         }
 
         if (DEBUG) logger.debug("\nPhasing table [AFTER CALCULATION]:\n" + sampleHaps + "\n");
-        MaxHaplotypeAndQuality maxHapQual = new MaxHaplotypeAndQuality(sampleHaps, true);
+        MaxHaplotypeAndQuality maxHapQual = new MaxHaplotypeAndQuality(sampleHaps, DEBUG);
         double posteriorProb = maxHapQual.maxEntry.getScore().getValue();
 
         if (DEBUG)
@@ -971,7 +972,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
         public MaxHaplotypeAndQuality(PhasingTable hapTable, boolean printDebug) {
             // Marginalize each haplotype to its first 2 positions:
             hapTable = HaplotypeTableCreator.marginalizeAsNewTable(hapTable);
-            if (DEBUG && printDebug)
+            if (printDebug)
                 logger.debug("\nPhasing table [AFTER MAPPING]:\n" + hapTable + "\n");
 
             calculateMaxHapAndPhasingQuality(hapTable, printDebug);
@@ -981,7 +982,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
 
         private void calculateMaxHapAndPhasingQuality(PhasingTable hapTable, boolean printDebug) {
             hapTable.normalizeScores();
-            if (DEBUG && printDebug)
+            if (printDebug)
                 logger.debug("\nPhasing table [AFTER NORMALIZATION]:\n" + hapTable + "\n");
 
             // Determine the phase at this position: