Added support for ngmlr

src/nanook/NanoOK.java

@@ -25,7 +25,7 @@
  * @author Richard Leggett
  */
 public class NanoOK {
-    public final static String VERSION_STRING = "v1.32";
+    public final static String VERSION_STRING = "v1.33";
     public final static long SERIAL_VERSION = 3L;
 
     /**

src/nanook/NanoOKOptions.java

@@ -209,7 +209,7 @@ public void parseArgs(String[] args) {
             System.out.println("    -force to force NanoOK to ignore warnings");
             System.out.println("    -timeout to set the number of seconds before giving up waiting for new reads (default 2)");
             System.out.println("");
-            System.out.println("Valid aligners: last, bwa, blasr, marginalign, graphmap, minimap2");
+            System.out.println("Valid aligners: last, bwa, blasr, marginalign, graphmap, minimap2, ngmlr");
             System.out.println("");
             System.exit(0);
         }
@@ -991,6 +991,9 @@ public AlignmentFileParser getParser() {
             case "minimap2":
                 parser = new Minimap2Parser(this, references);
                 break;
+            case "ngmlr":
+                parser = new NgmlrParser(this, references);
+                break;
             default:
                 System.out.println("Aligner unknown!");
                 System.out.println("");

src/nanook/NgmlrParser.java

@@ -0,0 +1,66 @@
+/*
+ * Program: NanoOK
+ * Author:  Richard M. Leggett
+ * 
+ * Copyright 2015 The Genome Analysis Centre (TGAC)
+ */
+
+package nanook;
+
+import java.io.File;
+
+/**
+ * Parser for Ngmlr files
+ * @author Richard Leggett
+ */
+public class NgmlrParser extends SAMParser implements AlignmentFileParser {
+    private String alignmentParams = "-x ont";
+    private NanoOKOptions options;
+
+    public NgmlrParser(NanoOKOptions o, References r) {
+        super(o, r);
+        options = o;
+    }
+
+    public String getProgramID() {
+        return "ngmlr";
+    }
+
+    public int getReadFormat() {
+        int or = options.getReadFormat();    
+        return or;
+
+        //return NanoOKOptions.FASTA;
+    }
+
+    public void setAlignmentParams(String p) {
+        alignmentParams = p;
+    }
+
+    public boolean outputsToStdout() {
+        return false;
+    }
+
+    public String getRunCommand(String query, String output, String reference) {
+        //reference = reference.replaceAll("\\.fasta$", "");
+        //reference = reference.replaceAll("\\.fa$", "");
+
+        return "ngmlr -r " + reference + " -q " + query + " -o "+output;
+    }
+
+    public void checkForIndex(String referenceFile) {
+        //File f = new File(referenceFile + ".fasta.mmi");
+
+        //System.out.println("Checking!!!");
+
+        //if (!f.exists()) {
+        //    System.out.println("");
+        //    System.out.println("Error:");
+        //    System.out.println("Can't find file " + f.getPath());
+        //    System.out.println("Have you indexed the reference with minimap2 -d ref.fasta.mmi ref.fasta?");
+        //    System.exit(1);
+        //}
+
+        return;
+    }    
+}