Minor refactoring of the cleaner allows me to add a trivial walker that left aligns the indels present in reads.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4581 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java

@@ -1071,7 +1071,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         return reduces;
     }
 
-    private static Cigar unclipCigar(Cigar cigar) {
+    protected static Cigar unclipCigar(Cigar cigar) {
         ArrayList<CigarElement> elements = new ArrayList<CigarElement>(cigar.numCigarElements());
         for ( CigarElement ce : cigar.getCigarElements() ) {
             if ( !isClipOperator(ce.getOperator()) )
@@ -1084,6 +1084,26 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         return op == CigarOperator.S || op == CigarOperator.H || op == CigarOperator.P;
     }
 
+    protected static Cigar reclipCigar(Cigar cigar, SAMRecord read) {
+        ArrayList<CigarElement> elements = new ArrayList<CigarElement>();
+
+        int i = 0;
+        int n = read.getCigar().numCigarElements();
+        while ( i < n && isClipOperator(read.getCigar().getCigarElement(i).getOperator()) )
+            elements.add(read.getCigar().getCigarElement(i++));
+
+        elements.addAll(cigar.getCigarElements());
+
+        i++;
+        while ( i < n && !isClipOperator(read.getCigar().getCigarElement(i).getOperator()) )
+            i++;
+
+        while ( i < n && isClipOperator(read.getCigar().getCigarElement(i).getOperator()) )
+            elements.add(read.getCigar().getCigarElement(i++));
+
+        return new Cigar(elements);
+    }
+
     private class AlignedRead {
         private final SAMRecord read;
         private byte[] readBases = null;
@@ -1191,23 +1211,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
         // pull out the bases that aren't clipped out
         private Cigar reclipCigar(Cigar cigar) {
-            ArrayList<CigarElement> elements = new ArrayList<CigarElement>();
+            return IndelRealigner.reclipCigar(cigar, read);
-
-            int i = 0;
-            int n = read.getCigar().numCigarElements();
-            while ( i < n && isClipOperator(read.getCigar().getCigarElement(i).getOperator()) )
-                elements.add(read.getCigar().getCigarElement(i++));
-
-            elements.addAll(cigar.getCigarElements());
-
-            i++;
-            while ( i < n && !isClipOperator(read.getCigar().getCigarElement(i).getOperator()) )
-                i++;
-
-            while ( i < n && isClipOperator(read.getCigar().getCigarElement(i).getOperator()) )
-                elements.add(read.getCigar().getCigarElement(i++));
-
-            return new Cigar(elements);
         }
 
         // tentatively sets the new start, but it needs to be confirmed later

java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java

@@ -0,0 +1,87 @@
+/*
+ * Copyright (c) 2010.
+ *
+ * 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.walkers.indels;
+
+import net.sf.samtools.*;
+import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+
+/**
+ * Left aligns indels in reads.
+ */
+public class LeftAlignIndels extends ReadWalker<Integer, Integer> {
+
+    @Output(required=false, doc="Output bam")
+    protected StingSAMFileWriter writer = null;
+
+    @Argument(fullName="maxReadsInRam", shortName="maxInRam", doc="max reads allowed to be kept in memory at a time by the SAMFileWriter. "+
+                "If too low, the tool may run out of system file descriptors needed to perform sorting; if too high, the tool may run out of memory.", required=false)
+    protected int MAX_RECORDS_IN_RAM = 500000;
+
+    public void initialize() {
+        // set up the output writer
+        if ( writer != null )
+            writer.setMaxRecordsInRam(MAX_RECORDS_IN_RAM);
+    }
+
+    private void emit(final SAMRecord read) {
+        if ( writer != null )
+            writer.addAlignment(read);
+    }
+
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+        // we can not deal with screwy records
+        if ( read.getCigar().numCigarElements() == 0 ) {
+            emit(read);
+            return 0;
+        }
+
+        // move existing indels (for 1 indel reads only) to leftmost position within identical sequence
+        int numBlocks = AlignmentUtils.getNumAlignmentBlocks(read);
+        if ( numBlocks == 2 ) {
+            Cigar newCigar = AlignmentUtils.leftAlignIndel(IndelRealigner.unclipCigar(read.getCigar()), ref.getBases(), read.getReadBases(), 0, 0);
+            newCigar = IndelRealigner.reclipCigar(newCigar, read);
+            read.setCigar(newCigar);
+        }
+
+        emit(read);
+        return 1;
+    }
+
+    public Integer reduceInit() {
+        return 0;
+    }
+
+    public Integer reduce(Integer value, Integer sum) {
+        return sum + value;
+    }
+
+    public void onTraversalDone(Integer result) {}
+}