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

For some reason I wasn't allowing expressions to be used with the -all argument. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5652 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-04-15 20:59:10 +00:00
parent 2cf6a06503
commit 1c32deb108
2 changed files with 5 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -137,7 +137,8 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
if ( USE_ALL_ANNOTATIONS ) if ( USE_ALL_ANNOTATIONS )
engine = new VariantAnnotatorEngine(getToolkit()); engine = new VariantAnnotatorEngine(getToolkit());
else else
engine = new VariantAnnotatorEngine(getToolkit(), annotationGroupsToUse, annotationsToUse, expressionsToUse); engine = new VariantAnnotatorEngine(getToolkit(), annotationGroupsToUse, annotationsToUse);
engine.initializeExpressions(expressionsToUse);
// setup the header fields // setup the header fields
// note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones // note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones

9
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
View File

@ -96,17 +96,14 @@ public class VariantAnnotatorEngine {
initializeDBs(engine); initializeDBs(engine);
} }
// use this constructor if you want to select specific annotations (and/or interfaces), but no expressions // use this constructor if you want to select specific annotations (and/or interfaces)
public VariantAnnotatorEngine(GenomeAnalysisEngine engine, List<String> annotationGroupsToUse, List<String> annotationsToUse) { public VariantAnnotatorEngine(GenomeAnalysisEngine engine, List<String> annotationGroupsToUse, List<String> annotationsToUse) {
initializeAnnotations(annotationGroupsToUse, annotationsToUse); initializeAnnotations(annotationGroupsToUse, annotationsToUse);
initializeDBs(engine); initializeDBs(engine);
} }
// use this constructor if you want to select specific annotations (and/or interfaces) plus expressions // select specific expressions to use
public VariantAnnotatorEngine(GenomeAnalysisEngine engine, List<String> annotationGroupsToUse, List<String> annotationsToUse, List<String> expressionsToUse) { public void initializeExpressions(List<String> expressionsToUse) {
initializeAnnotations(annotationGroupsToUse, annotationsToUse);
initializeDBs(engine);
// set up the expressions // set up the expressions
for ( String expression : expressionsToUse ) for ( String expression : expressionsToUse )
requestedExpressions.add(new VAExpression(expression)); requestedExpressions.add(new VAExpression(expression));