From 02f1af0743a8037c366dc3591e7c0fdebac0fd41 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 10 Aug 2009 03:10:33 +0000
Subject: [PATCH] Don't die when a readgroup is absent from the covariates
 table - it could happen when all reads are unmapped (or have MQ0); instead,
 just don't alter the quals.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1394 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../recalibration/TableRecalibrationWalker.java       | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index 3fe68eb21..08a09f4d1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -292,7 +292,16 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
         byte[] recalQuals = new byte[quals.length];
         RecalMapping mapper = cache.get(readGroup);
-        if ( mapper == null ) { throw new StingException(String.format("BUG: couldn't find RecalMapping for readgroup %s", readGroup)); }
+        if ( mapper == null ) {
+            // throw new StingException(String.format("BUG: couldn't find RecalMapping for readgroup %s", readGroup));
+            // Edited by ebanks on 8/9/09
+            // Actually, there is a valid case when the mapper == null: when all reads in a RG are
+            // unmapped or have mapping quality == 0.  In this case, we don't want to die - nor do we
+            // want to lose these reads - so we just don't alter the quals
+            for ( int cycle = 0; cycle < bases.length; cycle++ )
+                recalQuals[cycle] = quals[cycle];
+            return recalQuals;
+        }
 
         recalQuals[0] = quals[0];               // can't change the first -- no dinuc
         for ( int cycle = 1; cycle < bases.length; cycle++ ) { // skip first and last base, qual already set because no dinuc