We need to sort cleaned reads ourselves (instead of letting SAMFileWriter

do it) because the SAM headers are often screwed up and claim to be
"unsorted".  While here, I broke off the module from the SortSamIterator
in case someone else wants to use it.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@654 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/iterators/SortSamIterator.java

@@ -1,21 +1,13 @@
 package org.broadinstitute.sting.gatk.iterators;
 
+import org.broadinstitute.sting.utils.ComparableSAMRecord;
+
 import net.sf.samtools.SAMRecord;
 
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Iterator;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
-
-/**
- * Created by IntelliJ IDEA.
- * User: mdepristo
- * Date: Mar 15, 2009
- * Time: 6:02:31 PM
- * To change this template use File | Settings | File Templates.
- */
 public class SortSamIterator implements Iterator<SAMRecord> {
 
     Iterator<ComparableSAMRecord> it;
@@ -25,9 +17,9 @@ public class SortSamIterator implements Iterator<SAMRecord> {
         ArrayList<ComparableSAMRecord> list = new ArrayList<ComparableSAMRecord>();
         while (unsortedIter.hasNext()) {
             list.add(new ComparableSAMRecord(unsortedIter.next()));
-            // choose an arbitrary length to limit sorting for now
+            // limit how much can be sorted for now
             if (list.size() > maxSorts)
-                throw new UnsupportedOperationException("Can not sort files with more than 100K reads on the fly!");
+                throw new UnsupportedOperationException("Can not sort files with more than " + maxSorts + " reads on the fly!");
         }
         Collections.sort(list);
         it = list.iterator();
@@ -39,23 +31,4 @@ public class SortSamIterator implements Iterator<SAMRecord> {
     public void remove() {
         throw new UnsupportedOperationException("Can not remove records from a SAM file via an iterator!");
     }
-
-    private class ComparableSAMRecord implements Comparable<ComparableSAMRecord> {
-
-        private SAMRecord record;
-
-        public ComparableSAMRecord(SAMRecord record) {
-            this.record = record;
-        }
-
-        public SAMRecord getRecord() {
-            return record;
-        }
-
-        public int compareTo(ComparableSAMRecord o) {
-            GenomeLoc myLoc = new GenomeLoc(record);
-            GenomeLoc hisLoc = new GenomeLoc(o.getRecord());
-            return myLoc.compareTo(hisLoc);
-        }
-    }
 }

java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java

@@ -2,6 +2,7 @@
 package org.broadinstitute.sting.playground.gatk.walkers;
 
 import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.ComparableSAMRecord;
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.walkers.LocusWindowWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
@@ -11,8 +12,7 @@ import org.broadinstitute.sting.playground.indels.*;
 
 import net.sf.samtools.*;
 
-import java.util.ArrayList;
+import java.util.*;
-import java.util.List;
 import java.io.File;
 
 @WalkerName("IntervalCleaner")
@@ -27,10 +27,13 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
     public static final int MAX_QUAL = 99;
 
     private SAMFileWriter writer;
+    // we need to sort the reads ourselves because SAM headers get messed up and claim to be "unsorted" sometimes
+    private TreeSet<ComparableSAMRecord> readsToWrite;
 
     public void initialize() {
         SAMFileHeader header = getToolkit().getSamReader().getFileHeader();
         writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, false, new File(OUT));
+        readsToWrite = new TreeSet<ComparableSAMRecord>();
     }
 
     // do we care about reads that are not part of our intervals?
@@ -54,7 +57,7 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
                  read.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START )
                 goodReads.add(read);
             else
-                writer.addAlignment(read);
+                readsToWrite.add(new ComparableSAMRecord(read));
         }
 
         clean(goodReads, ref, context.getLocation().getStart());
@@ -62,6 +65,9 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
         //testCleanWithDeletion();
         //testCleanWithInsertion();
 
+        Iterator<ComparableSAMRecord> iter = readsToWrite.iterator();
+        while ( iter.hasNext() )
+            writer.addAlignment(iter.next().getRecord());
         return 1;
     }
 
@@ -198,13 +204,13 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
             // clean the appropriate reads
             for ( Pair<Integer, Integer> indexPair : bestConsensus.readIndexes )
                 updateRead(bestConsensus.cigar, bestConsensus.positionOnReference, indexPair.getSecond(), altReads.get(indexPair.getFirst()), (int)leftmostIndex);
+        }
 
         // write them out
         for ( SAMRecord rec : refReads )
-                writer.addAlignment(rec);
+            readsToWrite.add(new ComparableSAMRecord(rec));
         for ( AlignedRead aRec : altReads )
-                writer.addAlignment(aRec.getRead());           
+            readsToWrite.add(new ComparableSAMRecord(aRec.getRead()));
-        }
     }
 
     private Pair<Integer, Integer> findBestOffset(String ref, AlignedRead read) {
@@ -540,18 +546,18 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
         }
 
         // if the best alternate consensus has a smaller sum of quality score mismatches, then clean!
-        if ( bestConsensus.mismatchSum < totalMismatchSum ) {
+        if ( bestConsensus != null && bestConsensus.mismatchSum < totalMismatchSum ) {
             logger.info("CLEAN: " + bestConsensus.str);
 
             // clean the appropriate reads
             for ( Pair<Integer, Integer> indexPair : bestConsensus.readIndexes )
                 updateRead(bestConsensus.cigar, bestConsensus.positionOnReference, indexPair.getSecond(), altReads.get(indexPair.getFirst()), (int)leftmostIndex);
+        }
 
         // write them out
         for ( SAMRecord rec : refReads )
-                writer.addAlignment(rec);
+            readsToWrite.add(new ComparableSAMRecord(rec));
         for ( AlignedRead aRec : altReads )
-                writer.addAlignment(aRec.getRead());
+            readsToWrite.add(new ComparableSAMRecord(aRec.getRead()));
-        }
     }
 }

java/src/org/broadinstitute/sting/utils/ComparableSAMRecord.java

@@ -0,0 +1,28 @@
+package org.broadinstitute.sting.utils;
+
+import net.sf.samtools.SAMRecord;
+
+public class ComparableSAMRecord implements Comparable<ComparableSAMRecord> {
+
+    private SAMRecord record;
+
+    public ComparableSAMRecord(SAMRecord record) {
+        this.record = record;
+    }
+
+    public SAMRecord getRecord() {
+        return record;
+    }
+
+    public int compareTo(ComparableSAMRecord o) {
+        // first sort by start position
+        GenomeLoc myLoc = new GenomeLoc(record);
+        GenomeLoc hisLoc = new GenomeLoc(o.getRecord());
+        int comparison = myLoc.compareTo(hisLoc);
+        // if the reads have the same start position, we must give a non-zero comparison
+        // (because java Sets often require "consistency with equals")
+        if ( comparison == 0 )
+            comparison = record.getReadName().compareTo(o.getRecord().getReadName());
+        return comparison;
+    }
+}