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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mark DePristo 2011-10-06 08:17:08 -07:00
parent 4b5b9155a9 c649759978
commit 23845ac798
2 changed files with 10 additions and 4 deletions
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10
build.xml
View File

@ -547,10 +547,12 @@
<target name="vcf.jar" depends="gatk.compile,init.jar"> <target name="vcf.jar" depends="gatk.compile,init.jar">
<jar jarfile="${dist.dir}/vcf.jar"> <jar jarfile="${dist.dir}/vcf.jar">
<classfileset dir="${java.classes}"> <fileset dir="${java.classes}">
<rootfileset dir="${java.classes}" includes="org/broadinstitute/sting/utils/codecs/vcf/**/*.class" /> <include name="**/utils/codecs/**/*.class"/>
<rootfileset dir="${java.classes}" includes="org/broadinstitute/sting/utils/variantcontext/**/*.class" /> <include name="**/utils/variantcontext/**/*.class"/>
</classfileset> <include name="org/broadinstitute/sting/utils/exceptions/**"/>
<include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
</fileset>
</jar> </jar>
</target> </target>

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
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@ -130,6 +130,10 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
nVariantLoci++; nVariantLoci++;
nMixed++; nMixed++;
break; break;
case SYMBOLIC:
// ignore symbolic alleles, but don't fail
// todo - consistent way of treating symbolic alleles thgoughout codebase?
break;
default: default:
throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType()); throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
} }