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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
This commit is contained in:
hanna 2011-04-21 19:47:14 +00:00
parent 5b9a8555cd
commit 7428ae338a
3 changed files with 179 additions and 18 deletions
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18
java/src/net/sf/samtools/GATKBAMFileSpan.java
View File

@ -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.

78
java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
View File

@ -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.
Map.Entry<SAMReaderID,SAMFileSpan> entry = thisIterator.next();
combined.addFileSpans(entry.getKey(),entry.getValue());
}
else if(compareValue > 0) {
// Other before this.
Map.Entry<SAMReaderID,SAMFileSpan> entry = otherIterator.next();
combined.addFileSpans(entry.getKey(),entry.getValue());
}
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));
}
// This before other.
if(compareValue < 0)
mergeElementsInto(combined,thisIterator);
// Other before this.
else if(compareValue > 0)
mergeElementsInto(combined,otherIterator);
// equality; union the values.
else
mergeElementsInto(combined,thisIterator,otherIterator);
}
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);
}
}

101
java/test/org/broadinstitute/sting/gatk/datasources/reads/FilePointerUnitTest.java 100644
View File

@ -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");
}
}