127 lines
4.1 KiB
Java
127 lines
4.1 KiB
Java
package org.broadinstitute.sting.utils;
|
|
|
|
import static junit.framework.Assert.assertTrue;
|
|
import net.sf.samtools.SAMFileHeader;
|
|
import org.broadinstitute.sting.BaseTest;
|
|
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
|
|
import static org.junit.Assert.assertEquals;
|
|
import org.junit.Test;
|
|
|
|
|
|
/**
|
|
* @author aaron
|
|
* <p/>
|
|
* Class GenomeLocParserTest
|
|
* <p/>
|
|
* Test out the functionality of the new genome loc parser
|
|
*/
|
|
public class GenomeLocParserTest extends BaseTest {
|
|
|
|
@Test(expected = StingException.class)
|
|
public void testUnsetupException() {
|
|
GenomeLocParser.createGenomeLoc(0, 0, 0);
|
|
}
|
|
|
|
@Test
|
|
public void testKnownContigOrder() {
|
|
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10);
|
|
// assert that it's false when the contig ordering is not setup
|
|
assertTrue(!GenomeLocParser.hasKnownContigOrdering());
|
|
GenomeLocParser.setupRefContigOrdering(header.getSequenceDictionary());
|
|
// assert that it's true when it is setup
|
|
assertTrue(GenomeLocParser.hasKnownContigOrdering());
|
|
}
|
|
|
|
@Test(expected = RuntimeException.class)
|
|
public void testGetContigIndex() {
|
|
assertEquals(-1, GenomeLocParser.getContigIndex("blah")); // should be in the reference
|
|
}
|
|
|
|
@Test
|
|
public void testGetContigIndexValid() {
|
|
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10);
|
|
assertEquals(0, GenomeLocParser.getContigIndex("chr1")); // should be in the reference
|
|
}
|
|
|
|
@Test
|
|
public void testGetContigInfoUnknownContig() {
|
|
assertEquals(null, GenomeLocParser.getContigInfo("blah")); // should be in the reference
|
|
}
|
|
|
|
|
|
@Test
|
|
public void testGetContigInfoKnownContig() {
|
|
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10);
|
|
assertEquals("chr1".compareTo(GenomeLocParser.getContigInfo("chr1").getSequenceName()), 0); // should be in the reference
|
|
}
|
|
|
|
@Test(expected = StingException.class)
|
|
public void testParseBadString() {
|
|
GenomeLocParser.parseGenomeLoc("Bad:0-1");
|
|
}
|
|
|
|
@Test
|
|
public void testParseGoodString() {
|
|
GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1:1-100");
|
|
assertEquals(loc.getContigIndex(), 0);
|
|
assertEquals(100, loc.getStop());
|
|
assertEquals(1, loc.getStart());
|
|
}
|
|
|
|
@Test(expected = RuntimeException.class)
|
|
public void testParseBadLocations() {
|
|
GenomeLocParser.parseGenomeLocs("chr1:1-1;badChr:1-0");
|
|
}
|
|
|
|
@Test
|
|
public void testParseGoodLocations() {
|
|
GenomeLocParser.parseGenomeLocs("chr1:1-1;chr1:5-9");
|
|
}
|
|
|
|
@Test(expected = RuntimeException.class)
|
|
public void testParseGoodLocationsTooManySemiColons() {
|
|
GenomeLocParser.parseGenomeLocs("chr1:1-1;;chr1:5-9;");
|
|
}
|
|
|
|
@Test
|
|
public void testCreateGenomeLoc1() {
|
|
GenomeLoc loc = GenomeLocParser.createGenomeLoc("chr1", 1, 100);
|
|
assertEquals(loc.getContigIndex(), 0);
|
|
assertEquals(100, loc.getStop());
|
|
assertEquals(1, loc.getStart());
|
|
}
|
|
|
|
@Test
|
|
public void testCreateGenomeLoc2() {
|
|
GenomeLoc loc = GenomeLocParser.createGenomeLoc(0, 1, 100);
|
|
assertEquals(loc.getContigIndex(), 0);
|
|
assertEquals(100, loc.getStop());
|
|
assertEquals(1, loc.getStart());
|
|
}
|
|
|
|
@Test
|
|
public void testCreateGenomeLoc3() {
|
|
GenomeLoc loc = GenomeLocParser.createGenomeLoc(0, 1);
|
|
assertEquals(loc.getContigIndex(), 0);
|
|
assertEquals(1, loc.getStop());
|
|
assertEquals(1, loc.getStart());
|
|
}
|
|
|
|
@Test
|
|
public void testCreateGenomeLoc4() {
|
|
GenomeLoc loc = GenomeLocParser.createGenomeLoc("chr1", 1);
|
|
assertEquals(loc.getContigIndex(), 0);
|
|
assertEquals(1, loc.getStop());
|
|
assertEquals(1, loc.getStart());
|
|
}
|
|
|
|
@Test
|
|
public void testCreateGenomeLoc5() {
|
|
GenomeLoc loc = GenomeLocParser.createGenomeLoc(0,1,100);
|
|
GenomeLoc copy = GenomeLocParser.createGenomeLoc(loc);
|
|
assertEquals(copy.getContigIndex(), 0);
|
|
assertEquals(100, copy.getStop());
|
|
assertEquals(1, copy .getStart());
|
|
}
|
|
}
|