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Bugfix to compareTo and equals in GenomeLoc 

-- Yes, GenomeLoc.compareTo was broken.  The compareTo function only considered the contig and start position, but not the stop, when comparing genome locs.
-- Updated GenomeLoc.compareTo function to account for stop.  Updated GATK code where necessary to fix resulting problems that depended on this.
-- Added unit tests to ensure that hashcode, equals, and compareTo are all correct for GenomeLocs
This commit is contained in:
Mark DePristo 2012-08-30 15:07:02 -04:00
parent 5a9610d875
commit 7d95176539
3 changed files with 61 additions and 4 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
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@ -48,9 +48,7 @@ public class VerifyingSamIterator implements StingSAMIterator {
if(cur.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX || cur.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START)
throw new UserException.MalformedBAM(last,String.format("read %s has inconsistent mapping information.",cur.format()));
GenomeLoc lastLoc = genomeLocParser.createGenomeLoc( last );
GenomeLoc curLoc = genomeLocParser.createGenomeLoc( cur );
return curLoc.compareTo(lastLoc) == -1;
return last.getAlignmentStart() > cur.getAlignmentStart();
}
}

5
public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
View File

@ -427,7 +427,10 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Serializable, HasGenome
result = cmpContig;
} else {
if ( this.getStart() < that.getStart() ) result = -1;
if ( this.getStart() > that.getStart() ) result = 1;
else if ( this.getStart() > that.getStart() ) result = 1;
// these have the same start, so check the ends
else if ( this.getStop() < that.getStop() ) result = -1;
else if ( this.getStop() > that.getStop() ) result = 1;
}
}

56
public/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java
View File

@ -16,6 +16,7 @@ import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
@ -211,4 +212,59 @@ public class GenomeLocUnitTest extends BaseTest {
Assert.assertEquals(cfg.gl1.reciprocialOverlapFraction(cfg.gl2), cfg.overlapFraction);
}
}
// -------------------------------------------------------------------------------------
//
// testing comparison, hashcode, and equals
//
// -------------------------------------------------------------------------------------
@DataProvider(name = "GenomeLocComparisons")
public Object[][] createGenomeLocComparisons() {
List<Object[]> tests = new ArrayList<Object[]>();
final int start = 10;
for ( int stop = start; stop < start + 3; stop++ ) {
final GenomeLoc g1 = genomeLocParser.createGenomeLoc("chr2", start, stop);
for ( final String contig : Arrays.asList("chr1", "chr2", "chr3")) {
for ( int start2 = start - 1; start2 <= stop + 1; start2++ ) {
for ( int stop2 = start2; stop2 < stop + 2; stop2++ ) {
final GenomeLoc g2 = genomeLocParser.createGenomeLoc(contig, start2, stop2);
ComparisonResult cmp = ComparisonResult.EQUALS;
if ( contig.equals("chr3") ) cmp = ComparisonResult.LESS_THAN;
else if ( contig.equals("chr1") ) cmp = ComparisonResult.GREATER_THAN;
else if ( start < start2 ) cmp = ComparisonResult.LESS_THAN;
else if ( start > start2 ) cmp = ComparisonResult.GREATER_THAN;
else if ( stop < stop2 ) cmp = ComparisonResult.LESS_THAN;
else if ( stop > stop2 ) cmp = ComparisonResult.GREATER_THAN;
tests.add(new Object[]{g1, g2, cmp});
}
}
}
}
return tests.toArray(new Object[][]{});
}
private enum ComparisonResult {
LESS_THAN(-1),
EQUALS(0),
GREATER_THAN(1);
final int cmp;
private ComparisonResult(int cmp) {
this.cmp = cmp;
}
}
@Test(dataProvider = "GenomeLocComparisons")
public void testGenomeLocComparisons(GenomeLoc g1, GenomeLoc g2, ComparisonResult expected) {
Assert.assertEquals(g1.compareTo(g2), expected.cmp, "Comparing genome locs failed");
Assert.assertEquals(g1.equals(g2), expected == ComparisonResult.EQUALS);
if ( expected == ComparisonResult.EQUALS )
Assert.assertEquals(g1.hashCode(), g2.hashCode(), "Equal genome locs don't have the same hash code");
}
}