analysis: minor changes in RvTests analysis #125

opencb · Sep 19, 2017 · b9d862a · b9d862a
1 parent 360b56d
commit b9d862a
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/...alysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/RvTestsWrapper.java b/...alysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/RvTestsWrapper.java
@@ -16,8 +16,7 @@
 /**
  * Created by joaquin on 1/19/17.
  */
-//public class RvTestsWrapper extends AnalysisExecutor implements Serializable {
-public class RvTestsWrapper extends VariantAnalysisWrapper { // extends AnalysisExecutor implements Serializable {
+public class RvTestsWrapper extends VariantAnalysisWrapper {
     private String inFilename;
     private String metaFilename;
     private FilterParameters filterParams;
@@ -33,12 +32,12 @@ public RvTestsWrapper(String studyId, String inFilename, String metaFilename,
         this.filterParams = filterParams;
         this.rvtestsParams = rvtestsParams;
 
-        this.logger = LoggerFactory.getLogger(PlinkWrapper.class);
+        this.logger = LoggerFactory.getLogger(RvTestsWrapper.class);
     }
 
     @Override
     public void execute() throws AnalysisExecutorException {
-        // Sanity chek
+        // Sanity check
         if (binPath == null || !binPath.toFile().exists()) {
             String msg = "RvTests binary path is missing or does not exist:  '" + binPath + "'.";
             logger.error(msg);

diff --git a/...bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java b/...bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java
@@ -57,8 +57,8 @@ public void skat() {
             commandLine.append(" variant rvtests");
             commandLine.append(" --log-level ERROR");
             commandLine.append(" --dataset ").append(datasetName);
-            commandLine.append(" --rvtest-path ../../../soft/rvtests/executable/rvtest");
             commandLine.append(" -i ").append(avroPath);
+            commandLine.append(" --rvtests-path ../../../soft/rvtests/executable/rvtest");
             commandLine.append(" -Dsingle=wald");
             commandLine.append(" -Dout=/tmp/out.wald");
             VariantQueryCLITest.execute(commandLine.toString());