tools: rvtests implentation, #125

opencb · Jan 23, 2017 · c7ffbf2 · c7ffbf2
1 parent 0110fe6
commit c7ffbf2
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Showing 2 changed files with 8 additions and 6 deletions.
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
@@ -15,9 +15,11 @@ public class VariantRvTestsCLITest {
     Path confPath;
 
     private void init() throws URISyntaxException {
-        inPath = Paths.get("/home/jtarraga/data/vcf/skat/example.vcf.avro");
-        outPath = Paths.get("/home/jtarraga/data/vcf/skat/out");
-        confPath = Paths.get("/home/jtarraga/data/vcf/skat/skat.params");
+        String root = "/home/jtarraga/data100/vcf/rvtest-skat/spark";
+//        String root = "/home/jtarraga/data/vcf/skat/";
+        inPath = Paths.get(root + "/example.vcf.avro");
+        outPath = Paths.get(root + "/out");
+        confPath = Paths.get(root + "/skat.params");
     }
 
 //    @Test

diff --git a/...ta-tools/src/main/java/org/opencb/hpg/bigdata/tools/variant/analysis/RvTestsAnalysis.java b/...ta-tools/src/main/java/org/opencb/hpg/bigdata/tools/variant/analysis/RvTestsAnalysis.java
@@ -26,9 +26,9 @@ public class RvTestsAnalysis {
     private String outDirname;
     private String confFilename;
 
-    private final String RVTEST_BIN = "/home/jtarraga/softs/rvtests/executable/rvtest";
-    private final String BGZIP_BIN = "/home/joaquin/softs/htslib/bgzip";
-    private final String TABIX_BIN = "/home/joaquin/softs/htslib/tabix";
+    private final String RVTEST_BIN = "/home/jtarraga/soft/rvtests/executable/rvtest";
+    private final String BGZIP_BIN = "/usr/bin/bgzip"; //"/home/joaquin/softs/htslib/bgzip";
+    private final String TABIX_BIN = "/usr/bin/tabix"; //"/home/joaquin/softs/htslib/tabix";
 
     public RvTestsAnalysis(String inFilename, String outDirname, String confFilename) {
         this.inFilename = inFilename;