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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2012-11-27 11:00:50 -05:00
parent a82ec7ad80 4543ece088
commit 9531e58445
2 changed files with 21 additions and 2 deletions
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2
public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
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@ -374,7 +374,7 @@ public final class GenomeLocParser {
int start = 1; int start = 1;
int stop = -1; int stop = -1;
final int colonIndex = str.indexOf(":"); final int colonIndex = str.lastIndexOf(":");
if(colonIndex == -1) { if(colonIndex == -1) {
contig = str.substring(0, str.length()); // chr1 contig = str.substring(0, str.length()); // chr1
stop = Integer.MAX_VALUE; stop = Integer.MAX_VALUE;

21
public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java
View File

@ -2,6 +2,8 @@ package org.broadinstitute.sting.utils;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
@ -74,6 +76,23 @@ public class GenomeLocParserUnitTest extends BaseTest {
genomeLocParser.parseGenomeLoc("Bad:0-1"); genomeLocParser.parseGenomeLoc("Bad:0-1");
} }
@Test
public void testContigHasColon() {
SAMFileHeader header = new SAMFileHeader();
header.setSortOrder(net.sf.samtools.SAMFileHeader.SortOrder.coordinate);
SAMSequenceDictionary dict = new SAMSequenceDictionary();
SAMSequenceRecord rec = new SAMSequenceRecord("c:h:r1", 10);
rec.setSequenceLength(10);
dict.addSequence(rec);
header.setSequenceDictionary(dict);
final GenomeLocParser myGenomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
GenomeLoc loc = myGenomeLocParser.parseGenomeLoc("c:h:r1:4-5");
assertEquals(0, loc.getContigIndex());
assertEquals(loc.getStart(), 4);
assertEquals(loc.getStop(), 5);
}
@Test @Test
public void testParseGoodString() { public void testParseGoodString() {
GenomeLoc loc = genomeLocParser.parseGenomeLoc("chr1:1-10"); GenomeLoc loc = genomeLocParser.parseGenomeLoc("chr1:1-10");
@ -81,7 +100,7 @@ public class GenomeLocParserUnitTest extends BaseTest {
assertEquals(loc.getStop(), 10); assertEquals(loc.getStop(), 10);
assertEquals(loc.getStart(), 1); assertEquals(loc.getStart(), 1);
} }
@Test @Test
public void testCreateGenomeLoc1() { public void testCreateGenomeLoc1() {
GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1", 1, 100); GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1", 1, 100);