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make the size of a GenomeLoc int instead of long 

it will never be bigger than an int and it's actually useful to be an int so we can use it as parameters to array/list/hash size creation.
This commit is contained in:
Mauricio Carneiro 2012-02-01 19:34:39 -05:00
parent 5af3999a2d
commit e1d69e4060
3 changed files with 7 additions and 8 deletions
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2
public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
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@ -436,7 +436,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Serializable, HasGenome
* never be < 1. * never be < 1.
*/ */
@Ensures("result > 0") @Ensures("result > 0")
public long size() { public int size() {
return stop - start + 1; return stop - start + 1;
} }

4
public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
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@ -314,10 +314,10 @@ public class IntervalUtils {
* @param reference The reference for the intervals. * @param reference The reference for the intervals.
* @return A map of contig names with their sizes. * @return A map of contig names with their sizes.
*/ */
public static Map<String, Long> getContigSizes(File reference) { public static Map<String, Integer> getContigSizes(File reference) {
ReferenceDataSource referenceSource = new ReferenceDataSource(reference); ReferenceDataSource referenceSource = new ReferenceDataSource(reference);
List<GenomeLoc> locs = GenomeLocSortedSet.createSetFromSequenceDictionary(referenceSource.getReference().getSequenceDictionary()).toList(); List<GenomeLoc> locs = GenomeLocSortedSet.createSetFromSequenceDictionary(referenceSource.getReference().getSequenceDictionary()).toList();
Map<String, Long> lengths = new LinkedHashMap<String, Long>(); Map<String, Integer> lengths = new LinkedHashMap<String, Integer>();
for (GenomeLoc loc: locs) for (GenomeLoc loc: locs)
lengths.put(loc.getContig(), loc.size()); lengths.put(loc.getContig(), loc.size());
return lengths; return lengths;

9
public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
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@ -8,13 +8,12 @@ import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.commandline.IntervalBinding; import org.broadinstitute.sting.commandline.IntervalBinding;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource; import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.testng.Assert;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.testng.Assert;
import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider; import org.testng.annotations.DataProvider;
import org.testng.annotations.Test; import org.testng.annotations.Test;
@ -341,7 +340,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
@Test @Test
public void testGetContigLengths() { public void testGetContigLengths() {
Map<String, Long> lengths = IntervalUtils.getContigSizes(new File(BaseTest.hg18Reference)); Map<String, Integer> lengths = IntervalUtils.getContigSizes(new File(BaseTest.hg18Reference));
Assert.assertEquals((long)lengths.get("chr1"), 247249719); Assert.assertEquals((long)lengths.get("chr1"), 247249719);
Assert.assertEquals((long)lengths.get("chr2"), 242951149); Assert.assertEquals((long)lengths.get("chr2"), 242951149);
Assert.assertEquals((long)lengths.get("chr3"), 199501827); Assert.assertEquals((long)lengths.get("chr3"), 199501827);