From 0892daddb01dee51d8fa0b284ce932a87da8f6bf Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 1 Dec 2010 04:36:44 +0000
Subject: [PATCH] Improvement for the TGEN folks: when running in the solid
 recal mode of SET_Q_ZERO_BASE_N, update the NM tag if one was present in the
 read to reflect the new N's in the read.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4761 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/recalibration/TableRecalibrationWalker.java     | 6 +++++-
 1 file changed, 5 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 7c0e337fd..ebeb159f0 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -386,10 +386,14 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
             read.setAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, SAMUtils.phredToFastq(originalQuals));
         }
 
-        if (read.getAttribute(SAMTag.UQ.name()) != null && refBases != null && ! skipUQUpdate ) {
+        if (! skipUQUpdate && refBases != null && read.getAttribute(SAMTag.UQ.name()) != null) {
             read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, refBases.getBases(), read.getAlignmentStart() - 1, false));
         }
 
+        if (RAC.SOLID_RECAL_MODE == RecalDataManager.SOLID_RECAL_MODE.SET_Q_ZERO_BASE_N && refBases != null && read.getAttribute(SAMTag.NM.name()) != null) {
+            read.setAttribute(SAMTag.NM.name(), SequenceUtil.calculateSamNmTag(read, refBases.getBases(), read.getAlignmentStart() - 1, false));
+        }
+
         return read;
     }