Useful tool for calculating the perentage of misaligned reads at homozygous non-ref indel sites

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4013 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java

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+/*
+ * 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.oneoffprojects.walkers;
+
+import net.sf.samtools.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.*;
+import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
+import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.filters.BadMateFilter;
+import org.broad.tribble.util.variantcontext.VariantContext;
+
+import java.util.*;
+
+@By(DataSource.READS)
+@Requires(value={},referenceMetaData=@RMD(name="indels", type=ReferenceOrderedDatum.class))
+// walker to count reads that are and are not consistent with homozygous indels
+public class IndelConsistencyReadCounter extends ReadWalker<Integer, Integer> {
+
+    private long consistentReads = 0, misalignedReads = 0;
+
+    public boolean filter(ReferenceContext ref, SAMRecord read) {
+        return !doNotTryToClean(read);
+    }
+
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+        VariantContext indel = null;
+        for ( Collection<GATKFeature> rods : metaDataTracker.getContigOffsetMapping().values() ) {
+            Iterator<GATKFeature> rodIter = rods.iterator();
+            while ( rodIter.hasNext() ) {
+                Object rod = rodIter.next().getUnderlyingObject();
+                if ( VariantContextAdaptors.canBeConvertedToVariantContext(rod)) {
+                    VariantContext vc = VariantContextAdaptors.toVariantContext("", rod, ref);
+                    if ( vc.getName().equals("indels") ) {
+                        indel = vc;
+                        break;
+                    }
+                }
+            }
+        }
+
+        if ( indel != null ) {
+            if ( !containsAnyIndel(read) || !containsIndel(read, indel) )
+                misalignedReads++;
+            else
+                consistentReads++;
+        }
+
+        return 0;
+    }
+
+    private boolean doNotTryToClean(SAMRecord read) {
+        return read.getReadUnmappedFlag() ||
+                read.getNotPrimaryAlignmentFlag() ||
+                read.getReadFailsVendorQualityCheckFlag() ||
+                read.getMappingQuality() == 0 ||
+                read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ||
+                (BadMateFilter.hasBadMate(read));
+    }
+
+    private static boolean containsAnyIndel(final SAMRecord r) {
+        final Cigar cigar = r.getCigar();
+        if ( cigar == null )
+            return false;
+
+        for ( final CigarElement e : cigar.getCigarElements() ) {
+        	if (e.getOperator() == CigarOperator.D || e.getOperator() == CigarOperator.I )
+                return true;
+        }
+
+    	return false;
+    }
+
+    private static boolean containsIndel(final SAMRecord r, final VariantContext vc) {
+        int indelStart = vc.getStart() + 1;
+        int readPos = r.getAlignmentStart();
+        final Cigar cigar = r.getCigar();
+
+        int idx = 0;
+        while ( readPos < indelStart && idx < cigar.numCigarElements() ) {
+
+            final CigarElement ce = cigar.getCigarElement(idx);
+            switch ( ce.getOperator() ) {
+                case M:
+                case I:
+                case S:
+                    readPos += ce.getLength();
+                    break;
+                default:
+                    break;
+            }
+
+            idx++;
+        }
+
+        if ( idx == cigar.numCigarElements() )
+            return false;
+
+        if ( readPos != indelStart )
+            return false;
+
+        final CigarElement ce = cigar.getCigarElement(idx);
+        if ( vc.isDeletion() )
+            return ( ce.getOperator() == CigarOperator.D && ce.getLength() == vc.getReference().getBases().length);
+        return ( ce.getOperator() == CigarOperator.I && ce.getLength() == vc.getAlternateAllele(0).getBases().length);
+    }
+
+    public Integer reduceInit() {
+        return 0;
+    }
+
+    public Integer reduce(Integer value, Integer sum) {
+        return sum + value;
+    }
+
+    public void onTraversalDone(Integer result) {
+        System.out.println(consistentReads + " reads were initially consistent");
+        System.out.println(misalignedReads + " reads were initially misaligned");
+    }
+}