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fixing a couple of commented out portions of the VCFReader test 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3219 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-04-20 22:20:35 +00:00
parent 6fda78f93f
commit 4e18c54bb8
1 changed files with 3 additions and 3 deletions
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6
java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderUnitTest.java
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@ -318,19 +318,19 @@ public class VCFReaderUnitTest extends BaseTest {
rec = reader.next(); rec = reader.next();
Assert.assertTrue(!rec.isFiltered()); Assert.assertTrue(!rec.isFiltered());
Assert.assertTrue(rec.getFilterString().equals(".")); Assert.assertTrue(rec.getFilterString().equals("."));
// TODO: Aaron fix me Assert.assertEquals(Variation.VARIANT_TYPE.SNP, rec.getType()); Assert.assertEquals(VCFGenotypeEncoding.TYPE.SINGLE_BASE, rec.getType());
// record #9: deletion // record #9: deletion
if (!reader.hasNext()) Assert.fail("The reader should have a record"); if (!reader.hasNext()) Assert.fail("The reader should have a record");
rec = reader.next(); rec = reader.next();
// TODO: Aaron fix me Assert.assertEquals(Variation.VARIANT_TYPE.DELETION, rec.getType()); Assert.assertEquals(VCFGenotypeEncoding.TYPE.DELETION, rec.getType());
Assert.assertEquals(1, rec.getAlternateAlleleList().size()); Assert.assertEquals(1, rec.getAlternateAlleleList().size());
Assert.assertTrue(rec.getAlternateAlleleList().get(0).equals("")); Assert.assertTrue(rec.getAlternateAlleleList().get(0).equals(""));
// record #10: insertion // record #10: insertion
if (!reader.hasNext()) Assert.fail("The reader should have a record"); if (!reader.hasNext()) Assert.fail("The reader should have a record");
rec = reader.next(); rec = reader.next();
// TODO: Aaron fix me Assert.assertEquals(Variation.VARIANT_TYPE.INSERTION, rec.getType()); Assert.assertEquals(VCFGenotypeEncoding.TYPE.INSERTION, rec.getType());
Assert.assertEquals(rec.getAlternateAlleleList().size(), 1); Assert.assertEquals(rec.getAlternateAlleleList().size(), 1);
Assert.assertTrue(rec.getAlternateAlleleList().get(0).equals("CAT")); Assert.assertTrue(rec.getAlternateAlleleList().get(0).equals("CAT"));