In TableRecalibrationWalker, update UQ tag if it was present in the original SAMRecord. This required a new sam.jar, which caused some other files to need to be changed.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2435 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java

@@ -58,6 +58,10 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
         writer.addAlignment(read);
     }
 
+    public SAMFileHeader getFileHeader() {
+        return writer.getFileHeader();
+    }
+
     public void close() {
         writer.close();
     }

java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java

@@ -89,6 +89,10 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, SAMFileWriter {
         return engine.getSAMFileHeader();    
     }
 
+    public SAMFileHeader getFileHeader() {
+        return getSAMFileHeader();
+    }
+
     /**
      * Retrieves the desired compression level for 
      * @return The current compression level.  Could be null if the user doesn't care.

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.*;
+import net.sf.samtools.util.SequenceUtil;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.gatk.walkers.Requires;
@@ -336,6 +337,10 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         if ( read.getAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG) == null ) { // Save the old qualities if the tag isn't already taken in the read
             read.setAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, QualityUtils.phredToFastq(originalQuals));
         }
+        if (read.getAttribute(SAMTag.UQ.name()) != null) {
+            // TODO - When refBases is switches to byte[], call the appropriate overload in SAM-JDK, and remove char[] overload from SAM-JDK.
+            read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, refBases, read.getAlignmentStart() - 1));
+        }
 
         return read;
     }

java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriter.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.utils.sam;
 
+import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMRecord;
 
@@ -52,6 +53,13 @@ public class ArtificialSAMFileWriter implements SAMFileWriter {
         records.add(alignment);
     }
 
+    public SAMFileHeader getFileHeader() {
+        if (records.size() > 0) {
+            return records.get(0).getHeader();
+        }
+        return null;
+    }
+
     /** not much to do when we're fake */
     public void close() {
         closed = true;

settings/repository/net.sf/sam-1.07.168.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.07.168" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.11.221.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.11.221" status="release" />
+</ivy-module>