Improve format of output files

src/main/java/genepi/imputationserver/steps/InputValidationCommand.java

@@ -63,7 +63,7 @@ public class InputValidationCommand implements Callable<Integer> {
 	private OutputWriter output = null;
 
 	public InputValidationCommand() {
-		VcfFileUtil.setTabixBinary("tabix");
+
 	}
 
 	public void setFiles(List<String> files) {
@@ -118,10 +118,6 @@ public void setContactEmail(String contactEmail) {
 		this.contactEmail = contactEmail;
 	}
 
-	protected void setupTabix(String path) {
-		VcfFileUtil.setTabixBinary(path);
-	}
-
 	@Override
 	public Integer call() throws Exception {
 

src/main/java/genepi/imputationserver/steps/PrepareTraceCommand.java

@@ -48,11 +48,7 @@ public class PrepareTraceCommand implements Callable<Integer> {
 	private OutputWriter outputWriter = null;
 
 	public PrepareTraceCommand() {
-		VcfFileUtil.setTabixBinary("tabix");
-	}
 
-	protected void setupTabix(String path) {
-		VcfFileUtil.setTabixBinary(path);
 	}
 
 	@Override
@@ -93,7 +89,7 @@ public boolean prepareTraceJobs() throws Exception {
 				task.setVcfFilenames(files);
 				task.setChainFile(fullPathChainFile);
 				task.setChunksDir(chunksDir);
-				task.setExcludedSnpsWriter(null);
+				task.setStatDir(output);
 
 				TaskResults results = runTask(outputWriter, task);