A fix for Marian Thieme's NPE in the new sharding system.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5675 348d0f76-0448-11de-a6fe-93d51630548a

java/src/net/sf/samtools/GATKBAMFileSpan.java

@@ -64,6 +64,24 @@ public class GATKBAMFileSpan extends BAMFileSpan {
         super(Arrays.<Chunk>asList(chunks));
     }
 
+    @Override
+    public boolean equals(final Object other) {
+        if(!(other instanceof BAMFileSpan))
+            return false;
+
+        List<Chunk> theseChunks = getChunks();
+        List<Chunk> otherChunks = ((BAMFileSpan)other).getChunks();
+
+        if(theseChunks.size() != otherChunks.size())
+            return false;
+        for(int i = 0; i < theseChunks.size(); i++) {
+            if(!theseChunks.get(i).equals(otherChunks.get(i)))
+                return false;
+        }
+
+        return true;
+    }
+
     /**
      * Gets the constituent chunks stored in this span.
      * @return An unmodifiable list of chunks.

java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java

@@ -30,6 +30,7 @@ import net.sf.samtools.SAMFileSpan;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
 
@@ -71,6 +72,33 @@ class FilePointer {
         this.isRegionUnmapped = false;
     }
 
+    @Override
+    public boolean equals(final Object other) {
+        if(!(other instanceof FilePointer))
+            return false;
+        FilePointer otherFilePointer = (FilePointer)other;
+
+        // intervals
+        if(this.locations.size() != otherFilePointer.locations.size())
+            return false;
+        for(int i = 0; i < locations.size(); i++) {
+            if(!this.locations.get(i).equals(otherFilePointer.locations.get(i)))
+                return false;
+        }
+
+        // fileSpans
+        if(this.fileSpans.size() != otherFilePointer.fileSpans.size())
+            return false;
+        Iterator<Map.Entry<SAMReaderID,SAMFileSpan>> thisEntries = this.fileSpans.entrySet().iterator();
+        Iterator<Map.Entry<SAMReaderID,SAMFileSpan>> otherEntries = otherFilePointer.fileSpans.entrySet().iterator();
+        while(thisEntries.hasNext() || otherEntries.hasNext()) {
+            if(!thisEntries.next().equals(otherEntries.next()))
+                return false;
+        }
+        
+        return true;
+    }
+
     public void addLocation(final GenomeLoc location) {
         locations.add(location);
     }
@@ -153,26 +181,40 @@ class FilePointer {
         PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>> otherIterator = new PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>>(other.fileSpans.entrySet().iterator());
 
         while(thisIterator.hasNext() || otherIterator.hasNext()) {
-            int compareValue = thisIterator.peek().getKey().compareTo(otherIterator.peek().getKey());
+            int compareValue;
+            if(!otherIterator.hasNext()) {
+                compareValue = -1;
+            }
+            else if(!thisIterator.hasNext())
+                compareValue = 1;
+            else
+                compareValue = thisIterator.peek().getKey().compareTo(otherIterator.peek().getKey());
 
-            if(compareValue < 0) {
+            // This before other.
-                // This before other.
+            if(compareValue < 0)
-                Map.Entry<SAMReaderID,SAMFileSpan> entry = thisIterator.next();
+                mergeElementsInto(combined,thisIterator);
-                combined.addFileSpans(entry.getKey(),entry.getValue());
+            // Other before this.
-            }
+            else if(compareValue > 0)
-            else if(compareValue > 0) {
+                mergeElementsInto(combined,otherIterator);
-                // Other before this.
+            // equality; union the values.
-                Map.Entry<SAMReaderID,SAMFileSpan> entry = otherIterator.next();
+            else
-                combined.addFileSpans(entry.getKey(),entry.getValue());
+                mergeElementsInto(combined,thisIterator,otherIterator);
-            }
-            else {
-                // equality; union the values.
-                SAMReaderID reader = thisIterator.peek().getKey();
-                GATKBAMFileSpan thisRegion = (GATKBAMFileSpan)thisIterator.next().getValue();
-                GATKBAMFileSpan otherRegion = (GATKBAMFileSpan)otherIterator.next().getValue();
-                combined.addFileSpans(reader,thisRegion.union(otherRegion));
-            }
         }
         return combined;
     }
+
+    /**
+     * Roll the next element in the iterator into the combined entry.
+     * @param combined Entry into which to roll the next element.
+     * @param iterators Sources of next elements.
+     */
+    private void mergeElementsInto(final FilePointer combined, Iterator<Map.Entry<SAMReaderID,SAMFileSpan>>... iterators) {
+        if(iterators.length == 0)
+            throw new ReviewedStingException("Tried to add zero elements to an existing file pointer.");
+        Map.Entry<SAMReaderID,SAMFileSpan> initialElement = iterators[0].next();
+        GATKBAMFileSpan fileSpan = (GATKBAMFileSpan)initialElement.getValue();
+        for(int i = 1; i < iterators.length; i++)
+            fileSpan = fileSpan.union((GATKBAMFileSpan)iterators[i].next().getValue());
+        combined.addFileSpans(initialElement.getKey(),fileSpan);
+    }
 }

java/test/org/broadinstitute/sting/gatk/datasources/reads/FilePointerUnitTest.java

@@ -0,0 +1,101 @@
+/*
+ * Copyright (c) 2011, 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.datasources.reads;
+
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.samtools.GATKBAMFileSpan;
+import net.sf.samtools.GATKChunk;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.commandline.Tags;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.testng.Assert;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+
+/**
+ *
+ */
+public class FilePointerUnitTest extends BaseTest {
+    private IndexedFastaSequenceFile seq;
+    private GenomeLocParser genomeLocParser;
+    private SAMReaderID readerID = new SAMReaderID("samFile",new Tags());
+
+    /**
+     * This function does the setup of our parser, before each method call.
+     * <p/>
+     * Called before every test case method.
+     */
+    @BeforeMethod
+    public void doForEachTest() throws FileNotFoundException {
+        // sequence
+        seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
+        genomeLocParser = new GenomeLocParser(seq.getSequenceDictionary());
+    }
+
+    @Test
+    public void testFilePointerCombineDisjoint() {
+        FilePointer one = new FilePointer(genomeLocParser.createGenomeLoc("chr1",1,5));
+        one.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,1)));
+        FilePointer two = new FilePointer(genomeLocParser.createGenomeLoc("chr1",6,10));
+        two.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(1,2)));
+
+        FilePointer result = new FilePointer(genomeLocParser.createGenomeLoc("chr1",1,10));
+        result.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,2)));
+
+        Assert.assertEquals(one.combine(genomeLocParser,two),result,"Combination of two file pointers is incorrect");
+        Assert.assertEquals(two.combine(genomeLocParser,one),result,"Combination of two file pointers is incorrect");
+    }
+
+    @Test
+    public void testFilePointerCombineJoint() {
+        FilePointer one = new FilePointer(genomeLocParser.createGenomeLoc("chr1",1,5));
+        one.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,2)));
+        FilePointer two = new FilePointer(genomeLocParser.createGenomeLoc("chr1",2,6));
+        two.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(1,3)));
+
+        FilePointer result = new FilePointer(genomeLocParser.createGenomeLoc("chr1",1,6));
+        result.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,3)));        
+
+        Assert.assertEquals(one.combine(genomeLocParser,two),result,"Combination of two file pointers is incorrect");
+        Assert.assertEquals(two.combine(genomeLocParser,one),result,"Combination of two file pointers is incorrect");
+    }
+
+    @Test
+    public void testFilePointerCombineOneSided() {
+        FilePointer filePointer = new FilePointer(genomeLocParser.createGenomeLoc("chr1",1,5));
+        filePointer.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,1)));
+        FilePointer empty = new FilePointer(genomeLocParser.createGenomeLoc("chr1",6,10));
+        // Do not add file spans to empty result
+
+        FilePointer result = new FilePointer(genomeLocParser.createGenomeLoc("chr1",1,10));
+        result.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,1)));
+        Assert.assertEquals(filePointer.combine(genomeLocParser,empty),result,"Combination of two file pointers is incorrect");
+        Assert.assertEquals(empty.combine(genomeLocParser,filePointer),result,"Combination of two file pointers is incorrect");
+    }
+}