From b9d862a009c5064620d742f353c6130a855eb1ab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Tue, 19 Sep 2017 12:09:14 +0100 Subject: [PATCH] analysis: minor changes in RvTests analysis #125 --- .../bigdata/analysis/variant/wrappers/RvTestsWrapper.java | 7 +++---- .../hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java | 2 +- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/RvTestsWrapper.java b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/RvTestsWrapper.java index 120ef27c..5bbda346 100644 --- a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/RvTestsWrapper.java +++ b/hpg-bigdata-analysis/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/hpg-bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java b/hpg-bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java index 6db59f9b..97fe8261 100644 --- a/hpg-bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java +++ b/hpg-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());