-Integration tests for walkers that use original quals.

-framework for pushing -OQ into GATK (not done)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3004 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -25,6 +25,8 @@ public class GATKSAMRecord extends SAMRecord {
 
     // the SAMRecord data we're caching
     private String mReadString = null;
+    private String mQualString = null;
+    private byte[] mQualities = null;
     private SAMReadGroupRecord mReadGroup = null;
     private boolean mNegativeStrandFlag;
     private boolean mUnmappedFlag;
@@ -50,16 +52,9 @@ public class GATKSAMRecord extends SAMRecord {
 
         // because attribute methods are declared to be final (and we can't overload them),
         // we need to actually set all of the attributes here
-
+        List<SAMTagAndValue> attributes = record.getAttributes();
-        // TODO -- remove this exception catch when Picard fixes its internal bug (PIC-291)
+        for ( SAMTagAndValue attribute : attributes )
-
+            setAttribute(attribute.tag, attribute.value);
-        try {
-            List<SAMTagAndValue> attributes = record.getAttributes();
-            for ( SAMTagAndValue attribute : attributes )
-                setAttribute(attribute.tag, attribute.value);
-        } catch (NullPointerException picardError) {
-            ; // do nothing
-        }
     }
 
     ///////////////////////////////////////////////////////////////////////////////
@@ -122,6 +117,27 @@ public class GATKSAMRecord extends SAMRecord {
         mSecondOfPairFlag = b;
     }
 
+    public byte[] getBaseQualities() {
+        if ( mQualities == null )
+            mQualities = mRecord.getBaseQualities();
+        return mQualities;
+    }
+
+    public String getBaseQualityString() {
+        if ( mQualString == null )
+            mQualString = mRecord.getBaseQualityString();
+        return mQualString;
+    }
+
+    public void setBaseQualities(byte[] bytes) {
+        mQualities = bytes;
+        mRecord.setBaseQualities(bytes);
+    }
+
+    public void setBaseQualityString(String s) {
+        mQualString = s;
+        mRecord.setBaseQualityString(s);
+    }
 
     /**
      * Checks whether an attribute has been set for the given key.
@@ -130,7 +146,7 @@ public class GATKSAMRecord extends SAMRecord {
      * individual GATKSAMRecords. These attributes exist in memory only,
      * and are never written to disk.
      *
-     * @param key
+     * @param key key
      * @return True if an attribute has been set for this key.
      */
     public boolean containsTemporaryAttribute(Object key) {
@@ -148,8 +164,9 @@ public class GATKSAMRecord extends SAMRecord {
      * individual GATKSAMRecords. These attributes exist in memory only,
      * and are never written to disk.
      *
-     * @param key
+     * @param key    key
-     * @param value
+     * @param value  value
+     * @return attribute
      */
     public Object setTemporaryAttribute(Object key, Object value) {
         if(temporaryAttributes == null) {
@@ -165,7 +182,7 @@ public class GATKSAMRecord extends SAMRecord {
      * individual GATKSAMRecords. These attributes exist in memory only,
      * and are never written to disk.
      *
-     * @param key
+     * @param key key
      * @return The value, or null.
      */
     public Object getTemporaryAttribute(Object key) {
@@ -182,7 +199,7 @@ public class GATKSAMRecord extends SAMRecord {
      * individual GATKSAMRecords. These attributes exist in memory only,
      * and are never written to disk.
      *
-     * @param key
+     * @param key key
      * @return The value that was associated with this key, or null.
      */
     public Object removeTemporaryAttribute(Object key) {
@@ -192,23 +209,6 @@ public class GATKSAMRecord extends SAMRecord {
          return null;
     }
 
-    /////////////////////////////////////////////////////////////////////
-    // *** The following methods are final and cannot be overridden ***//
-    /////////////////////////////////////////////////////////////////////
-
-    //public final Object getAttribute(String s) { return mRecord.getAttribute(s); }
-
-    //public final Integer getIntegerAttribute(java.lang.String s) { return mRecord.getIntegerAttribute(s); }
-
-    //public final Short getShortAttribute(String s) { return mRecord.getShortAttribute(s); }
-
-    //public final Byte getByteAttribute(java.lang.String s) { return mRecord.getByteAttribute(s); }
-
-    //public final void setAttribute(String s, Object o) { mRecord.setAttribute(s, o); }
-
-    //public final List<net.sf.samtools.SAMRecord.SAMTagAndValue> getAttributes() { return mRecord.getAttributes(); }
-
-
     /////////////////////////////////////////////////////////////////////////////////
     // *** The following methods just call the appropriate method in the record ***//
     /////////////////////////////////////////////////////////////////////////////////
@@ -225,14 +225,6 @@ public class GATKSAMRecord extends SAMRecord {
 
     public int getReadLength() { return mRecord.getReadLength(); }
 
-    public String getBaseQualityString() { return mRecord.getBaseQualityString(); }
-
-    public void setBaseQualityString(java.lang.String s) { mRecord.setBaseQualityString(s); }
-
-    public byte[] getBaseQualities() { return mRecord.getBaseQualities(); }
-
-    public void setBaseQualities(byte[] bytes) { mRecord.setBaseQualities(bytes); }
-
     public byte[] getOriginalBaseQualities() { return mRecord.getOriginalBaseQualities(); }
 
     public void setOriginalBaseQualities(byte[] bytes) { mRecord.setOriginalBaseQualities(bytes); }

java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java

@@ -78,6 +78,29 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
+    @Test
+    public void testCountCovariatesUseOriginalQuals() {
+        HashMap<String, String> e = new HashMap<String, String>();
+        e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "26ae1bede4f337901b6194753f6cf914");
+
+        for ( Map.Entry<String, String> entry : e.entrySet() ) {
+            String bam = entry.getKey();
+            String md5 = entry.getValue();
+
+            WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                    "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                            " -T CountCovariates" +
+                            " -I " + bam +
+                            " -L 1:1-1,000" +
+                            " -standard" +
+                            " -OQ" +
+                            " -recalFile %s",
+                    1, // just one output file
+                    Arrays.asList(md5));
+            executeTest("testCountCovariatesUseOriginalQuals", spec);
+        }
+    }
+
     @Test
     public void testTableRecalibratorMaxQ70() {
         HashMap<String, String> e = new HashMap<String, String>();

java/test/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalkersIntegrationTest.java

@@ -39,4 +39,18 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
     @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "fb77d3122df468a71e03ca92b69493f4"); }
     @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "24053a87b00c0bc2ddf420975e9fea4d"); }
     @Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "aeb67cca75285a68af8a965faa547e7f"); }
+
+    @Test
+    public void testUseOriginalQuals() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
+                        " -T ClipReads" +
+                        " -I " + validationDataLocation + "originalQuals.chr1.1-1K.bam" +
+                        " -L chr1:1-1,000" +
+                        " -OQ -QT 4" +
+                        " -o %s -ob %s",
+                2,
+                Arrays.asList("55c01ccc2e84481b22d3632cdb06c8ba", "f9b1347fabbc33bb24f7c7fa8dfb798b"));
+        executeTest("clipOriginalQuals", spec);
+    }
 }