Remove the adaptor sequence clipping read filter because it is dangerous (it breaks LocusIteratorByState). We'll bring it back to life when ReadTransformers are created. Instead, have the utility code return a new clipped SAMRecord (necessary so that we don't break SNP calling in UG when the indel caller tries to hard-clip the reads).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5629 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/filters/AdaptorSequenceFilter.java

@@ -1,44 +0,0 @@
-/*
- * Copyright (c) 2009 The Broad Institute
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.gatk.filters;
-
-import net.sf.picard.filter.SamRecordFilter;
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
-
-/**
- * This class doesn't actually filter out reads (it's really a ReadTransformer): it hard-clips the
- * reads to remove the adaptor sequences from them.
- *
- * @author ebanks, depristo
- * @version 0.1
- */
-
-public class AdaptorSequenceFilter implements SamRecordFilter {
-
-    public boolean filterOut(final SAMRecord rec) {
-        return ReadUtils.hardClipAdaptorSequence(rec);
-    }
-}

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

@@ -176,27 +176,41 @@ public class ReadUtils {
         return new Pair<Integer, Integer>(adaptorStart, adaptorEnd);
     }
 
-    // return true if the read needs to be completely clipped
+    /**
-    public static boolean hardClipAdaptorSequence(final SAMRecord rec, int adaptorLength) {
+     *
+     * @param rec  original SAM record
+     * @param adaptorLength  length of adaptor sequence
+     * @return a new read with adaptor sequence hard-clipped out or null if read is fully clipped
+     */
+    public static SAMRecord hardClipAdaptorSequence(final SAMRecord rec, int adaptorLength) {
 
         Pair<Integer, Integer> adaptorBoundaries = getAdaptorBoundaries(rec, adaptorLength);
+        SAMRecord result = rec;
+
         if ( adaptorBoundaries != null ) {
             if ( rec.getReadNegativeStrandFlag() && adaptorBoundaries.second >= rec.getAlignmentStart() && adaptorBoundaries.first < rec.getAlignmentEnd() )
-                return hardClipStartOfRead(rec, adaptorBoundaries.second);
+                result = hardClipStartOfRead(rec, adaptorBoundaries.second);
             else if ( !rec.getReadNegativeStrandFlag() && adaptorBoundaries.first <= rec.getAlignmentEnd() )
-                return hardClipEndOfRead(rec, adaptorBoundaries.first);
+                result = hardClipEndOfRead(rec, adaptorBoundaries.first);
         }
 
-        return false;
+        return result;
     }
 
     // return true if the read needs to be completely clipped
-    private static boolean hardClipStartOfRead(SAMRecord rec, int stopPosition) {
+    private static SAMRecord hardClipStartOfRead(SAMRecord oldRec, int stopPosition) {
 
-        if ( stopPosition >= rec.getAlignmentEnd() ) {
+        if ( stopPosition >= oldRec.getAlignmentEnd() ) {
             // BAM representation issue -- we can't clip away all bases in a read, just leave it alone and let the filter deal with it
             //System.out.printf("Entire read needs to be clipped: %50s %n", rec.getReadName());
-            return true;
+            return null;
+        }
+
+        SAMRecord rec;
+        try {
+            rec = (SAMRecord)oldRec.clone();
+        } catch (Exception e) {
+            return null;
         }
 
         //System.out.printf("Clipping start of read: %50s start=%d adaptorEnd=%d isize=%d %n",
@@ -261,16 +275,22 @@ public class ReadUtils {
         // adjust the start accordingly
         rec.setAlignmentStart(stopPosition + 1);
 
-        return false;
+        return rec;
     }
 
-    // return true if the read needs to be completely clipped
+    private static SAMRecord hardClipEndOfRead(SAMRecord oldRec, int startPosition) {
-    private static boolean hardClipEndOfRead(SAMRecord rec, int startPosition) {
 
-        if ( startPosition <= rec.getAlignmentStart() ) {
+        if ( startPosition <= oldRec.getAlignmentStart() ) {
             // BAM representation issue -- we can't clip away all bases in a read, just leave it alone and let the filter deal with it
             //System.out.printf("Entire read needs to be clipped: %50s %n", rec.getReadName());
-            return true;
+            return null;
+        }
+
+        SAMRecord rec;
+        try {
+            rec = (SAMRecord)oldRec.clone();
+        } catch (Exception e) {
+            return null;
         }
 
         //System.out.printf("Clipping end of read: %50s adaptorStart=%d end=%d isize=%d %n",
@@ -341,12 +361,17 @@ public class ReadUtils {
         // adjust the stop accordingly
         // rec.setAlignmentEnd(startPosition - 1);
 
-        return false;
+        return rec;
     }
 
     private static int DEFAULT_ADAPTOR_SIZE = 100;
 
-    public static boolean hardClipAdaptorSequence(final SAMRecord rec) {
+    /**
+     *
+     * @param rec  original SAM record
+     * @return a new read with adaptor sequence hard-clipped out or null if read is fully clipped
+     */
+    public static SAMRecord hardClipAdaptorSequence(final SAMRecord rec) {
         return hardClipAdaptorSequence(rec, DEFAULT_ADAPTOR_SIZE);
     }