zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Revert "Modified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames" 

After discussing this with Mark, it seems clear that the old version of the
VariantEval FunctionalClass stratification is preferable to this version.
By reverting, we maintain backwards compatibility with legacy output files
from the old GenomicAnnotator, and can add SnpEff support later without
breaking that backwards compatibility.

This reverts commit b44acd1abd9ab6eec37111a19fa797f9e2ca3326.
This commit is contained in:
David Roazen 2011-09-14 10:47:28 -04:00
parent e0c8c0ddcb
commit 3db457ed01
2 changed files with 36 additions and 24 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

53
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
View File

@ -2,29 +2,21 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.ArrayList;
import java.util.List;
/**
* Stratifies by low-, moderate-, and high-impact genomic effect using SnpEff annotations produced by VariantAnnotator
* Stratifies by nonsense, missense, silent, and all annotations in the input ROD, from the INFO field annotation.
*/
public class FunctionalClass extends VariantStratifier {
public static final String LOW_IMPACT_STATE_NAME = "low-impact";
public static final String MODERATE_IMPACT_STATE_NAME = "moderate-impact";
public static final String HIGH_IMPACT_STATE_NAME = "high-impact";
public static final String EFFECT_IMPACT_ATTRIBUTE_KEY = SnpEff.InfoFieldKey.EFF_IMPACT.toString();
@Override
public void initialize() {
states.add("all");
states.add(LOW_IMPACT_STATE_NAME);
states.add(MODERATE_IMPACT_STATE_NAME);
states.add(HIGH_IMPACT_STATE_NAME);
states.add("silent");
states.add("missense");
states.add("nonsense");
}
@ -33,17 +25,36 @@ public class FunctionalClass extends VariantStratifier {
relevantStates.add("all");
if ( eval != null && eval.isVariant() && eval.hasAttribute(EFFECT_IMPACT_ATTRIBUTE_KEY) ) {
String effectImpact = eval.getAttributeAsString(EFFECT_IMPACT_ATTRIBUTE_KEY);
if (eval != null && eval.isVariant()) {
String type = null;
if ( effectImpact.equals(SnpEff.EffectImpact.LOW.toString()) ) {
relevantStates.add(LOW_IMPACT_STATE_NAME);
if (eval.hasAttribute("refseq.functionalClass")) {
type = eval.getAttributeAsString("refseq.functionalClass");
} else if (eval.hasAttribute("refseq.functionalClass_1")) {
int annotationId = 1;
String key;
do {
key = String.format("refseq.functionalClass_%d", annotationId);
String newtype = eval.getAttributeAsString(key);
if ( newtype != null && !newtype.equalsIgnoreCase("null") &&
( type == null ||
( type.equals("silent") && !newtype.equals("silent") ) ||
( type.equals("missense") && newtype.equals("nonsense") ) )
) {
type = newtype;
}
annotationId++;
} while (eval.hasAttribute(key));
}
else if ( effectImpact.equals(SnpEff.EffectImpact.MODERATE.toString()) ) {
relevantStates.add(MODERATE_IMPACT_STATE_NAME);
}
else if ( effectImpact.equals(SnpEff.EffectImpact.HIGH.toString()) ) {
relevantStates.add(HIGH_IMPACT_STATE_NAME);
if (type != null) {
if (type.equals("silent")) { relevantStates.add("silent"); }
else if (type.equals("missense")) { relevantStates.add("missense"); }
else if (type.equals("nonsense")) { relevantStates.add("nonsense"); }
}
}

7
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -123,8 +123,9 @@ public class VariantEvalIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + hg19Reference,
"--eval " + validationDataLocation + "snpEff.AFR.unfiltered.VariantAnnotator.output.vcf",
"-R " + b37KGReference,
"--dbsnp " + b37dbSNP132,
"--eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -133,7 +134,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("e93b3d66a5c150cbf1ae4262ec075d2d")
Arrays.asList("e40b77e7ed6581328e373a24b93cd170")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
}