Merge branch 'main' of https://github.com/richardmleggett/MARTi

richardmleggett · Jun 15, 2023 · d496236 · d496236
2 parents dbc657c + 3dd8594
commit d496236
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/engine/src/main/java/uk/ac/earlham/marti/core/MARTiEngineOptions.java b/engine/src/main/java/uk/ac/earlham/marti/core/MARTiEngineOptions.java
@@ -148,7 +148,7 @@ public class MARTiEngineOptions implements Serializable {
     private String optionsFilename = null;
     private MARTiEngineOptionsFile engineOptionsFile = null;
     private String classifyingBlastName = null;
-    private boolean compressBlastFiles = false;
+    private boolean compressBlastFiles = true;
 
     public MARTiEngineOptions() {
         String osName = System.getProperty("os.name").toLowerCase();
@@ -310,9 +310,12 @@ public void parseArgs(String[] args) {
             } else if (args[i].equalsIgnoreCase("-options")) {
                 optionsFilename = args[i+1];
                 i+=2;
-            } else if (args[i].equalsIgnoreCase("-compressBlast")) {
+            } else if (args[i].equalsIgnoreCase("-compressblast")) {
                 compressBlastFiles = true;
                 i++;
+            } else if (args[i].equalsIgnoreCase("-dontcompressblast")) {
+                compressBlastFiles = false;
+                i++;
             } else {
                 int iCurrent = i;