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Bug fix: annotation values ar parsed as Doubles when they should be parsed as Integers due to implicit conversion. 

* Updated expected test data in which an integer annotation (MQ0) was formatted as a double.
This commit is contained in:
Michael McCowan 2013-09-23 14:26:24 -04:00
parent 5bbad75402
commit 5113e21437
2 changed files with 6 additions and 2 deletions
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2
protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -194,7 +194,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
" --excludeNonVariants -combineAnnotations -setKey null" + " --excludeNonVariants -combineAnnotations -setKey null" +
" -L 20:10,000,000-10,001,000", b37KGReference), " -L 20:10,000,000-10,001,000", b37KGReference),
1, 1,
Arrays.asList("2e15db35359144683f1e58e147362679")); Arrays.asList("0413f0725fc5ec3a4f1ee246f6cb3a2a"));
cvExecuteTest("combineSingleSamplePipelineGVCF", spec, true); cvExecuteTest("combineSingleSamplePipelineGVCF", spec, true);
} }

6
public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
View File

@ -891,7 +891,11 @@ public class GATKVariantContextUtils {
} }
try { try {
final String stringValue = value.toString(); final String stringValue = value.toString();
values.add(stringValue.contains(".") ? Double.parseDouble(stringValue) : Integer.parseInt(stringValue)); // Branch to avoid unintentional, implicit type conversions that occur with the ? operator.
if (stringValue.contains("."))
values.add(Double.parseDouble(stringValue));
else
values.add(Integer.parseInt(stringValue));
} catch (NumberFormatException e) { } catch (NumberFormatException e) {
badAnnotation = true; badAnnotation = true;
} }