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Using the simple VCBuilder constructor and then subsequently trying to modify attributes was throwing a NPE. This is easily solved (without a performance hit) by initializing the attributes map to an immutable Collections.emptyMap(). Added unit test to cover this case.

This commit is contained in:
Eric Banks 2012-08-22 12:54:29 -04:00
parent 9e76e8aa0b
commit 94540ccc27
2 changed files with 5 additions and 0 deletions
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1
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
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@ -94,6 +94,7 @@ public class VariantContextBuilder {
this.start = start; this.start = start;
this.stop = stop; this.stop = stop;
this.alleles = alleles; this.alleles = alleles;
this.attributes = Collections.emptyMap(); // immutable
toValidate.add(VariantContext.Validation.ALLELES); toValidate.add(VariantContext.Validation.ALLELES);
} }

4
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
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@ -750,6 +750,10 @@ public class VariantContextUnitTest extends BaseTest {
modified = new VariantContextBuilder(modified).attributes(null).attribute("AC", 1).make(); modified = new VariantContextBuilder(modified).attributes(null).attribute("AC", 1).make();
Assert.assertEquals(modified.getAttribute("AC"), 1); Assert.assertEquals(modified.getAttribute("AC"), 1);
// test the behavior when the builder's attribute object is not initialized
modified = new VariantContextBuilder(modified.getSource(), modified.getChr(), modified.getStart(), modified.getEnd(), modified.getAlleles()).attribute("AC", 1).make();
// test normal attribute modification
modified = new VariantContextBuilder(cfg.vc).attribute("AC", 1).make(); modified = new VariantContextBuilder(cfg.vc).attribute("AC", 1).make();
Assert.assertEquals(modified.getAttribute("AC"), 1); Assert.assertEquals(modified.getAttribute("AC"), 1);
modified = new VariantContextBuilder(modified).attribute("AC", 2).make(); modified = new VariantContextBuilder(modified).attribute("AC", 2).make();