1. Fixing a bug that Mark found where indel-containing clipped reads would get an original cigar tag even when they didn't actually get modified.

2. Added some useful logging messages.
3. Added a oneoffs walker to calculate the number of realigned reads and intervals containing them.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3860 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -275,14 +275,17 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 readsNotToClean.add(read);
             } else {
                 boolean wellCoveredInterval = readsToClean.add(read, ref.getBases());
-                if ( !wellCoveredInterval )
-                    abortCleanForCurrentInterval();                
+                if ( !wellCoveredInterval ) {
+                    logger.info("We are aborting the realignment in interval " + currentInterval + " because it is not fully covered by reads");
+                    abortCleanForCurrentInterval();
+                }
 
                 // add the rods to the list of known variants
                 populateKnownIndels(metaDataTracker, ref);
             }
 
             if ( readsToClean.size() + readsNotToClean.size() >= MAX_READS ) {
+                logger.info("We are aborting the realignment in interval " + currentInterval + " because there are too many reads (see --maxReadsForRealignment for details)");
                 abortCleanForCurrentInterval();
             }
         }
@@ -1126,8 +1129,10 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 cigar = reclipCigar(cigar);
 
             // no change?
-            if ( getCigar().equals(cigar) )
+            if ( read.getCigar().equals(cigar) ) {
+                newCigar = null;
                 return;
+            }
 
             // no indel?
             String str = cigar.toString();

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

@@ -0,0 +1,129 @@
+/*
+ * 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.utils.interval.IntervalMergingRule;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.*;
+import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.filters.BadMateFilter;
+import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.sting.commandline.Argument;
+
+import java.io.File;
+import java.util.*;
+
+@By(DataSource.READS)
+public class RealignedReadCounter extends ReadWalker<Integer, Integer> {
+
+    public static final String ORIGINAL_CIGAR_TAG = "OC";
+    public static final String ORIGINAL_POSITION_TAG = "OP";
+
+    @Argument(fullName="targetIntervals", shortName="targetIntervals", doc="intervals file output from RealignerTargetCreator", required=true)
+    protected String intervalsFile = null;
+
+    // the intervals input by the user
+    private Iterator<GenomeLoc> intervals = null;
+
+    // the current interval in the list
+    private GenomeLoc currentInterval = null;
+
+    private long updatedIntervals = 0, updatedReads = 0;
+    private boolean intervalWasUpdated = false;
+
+    public void initialize() {
+        // prepare to read intervals one-by-one, as needed (assuming they are sorted).
+        intervals = new IntervalFileMergingIterator( new File(intervalsFile), IntervalMergingRule.OVERLAPPING_ONLY );
+        currentInterval = intervals.hasNext() ? intervals.next() : null;
+    }
+
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+        if ( currentInterval == null ) {
+            return 0;
+        }
+
+        GenomeLoc readLoc = GenomeLocParser.createGenomeLoc(read);
+        // hack to get around unmapped reads having screwy locations
+        if ( readLoc.getStop() == 0 )
+            readLoc = GenomeLocParser.createGenomeLoc(readLoc.getContigIndex(), readLoc.getStart(), readLoc.getStart());
+
+        if ( readLoc.isBefore(currentInterval) || ReadUtils.is454Read(read) )
+            return 0;
+
+        if ( readLoc.overlapsP(currentInterval) ) {
+            if ( doNotTryToClean(read) )
+                return 0;
+
+            if ( read.getAttribute(ORIGINAL_CIGAR_TAG) != null ) {
+                String newCigar = (String)read.getAttribute(ORIGINAL_CIGAR_TAG);
+                // deal with an old bug
+                if ( read.getCigar().toString().equals(newCigar) ) {
+                    //System.out.println(currentInterval + ": " + read.getReadName() + " " + read.getCigarString() + " " + newCigar);
+                    return 0;
+                }
+
+                if ( !intervalWasUpdated ) {
+                    intervalWasUpdated = true;
+                    updatedIntervals++;
+                }
+                updatedReads++;
+
+            }
+        } else {
+            do {
+                intervalWasUpdated = false;
+                currentInterval = intervals.hasNext() ? intervals.next() : null;
+            } while ( currentInterval != null && currentInterval.isBefore(readLoc) );
+        }
+
+        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));
+    }
+
+    public Integer reduceInit() {
+        return 0;
+    }
+
+    public Integer reduce(Integer value, Integer sum) {
+        return sum + value;
+    }
+
+    public void onTraversalDone(Integer result) {
+        System.out.println(updatedIntervals + " intervals were updated");
+        System.out.println(updatedReads + " reads were updated");
+    }
+}