Fix off-by-one error. Fixes issue #4

CHANGES

@@ -1,4 +1,7 @@
 Revision history for MinCED
+0.1.6	18-Jul-2014
+		Fix off-by-one error in the gff output.
+		
 0.1.5   03-Apl-2014
 		Changed the behaviour of the '-spacers' option. Without any
 		output file given the behaviour is the same as before, creating

CRISPR.java

@@ -139,7 +139,7 @@ public String toGff(String sequenceName, String parentName) {
 	   String str = "";
 	   for (int m = 0; m < numRepeats(); m++) {
 		   int repeat_position = (repeatAt(m) + 1);
-		   int repeat_end = repeat_position + this.repeatLength();
+		   int repeat_end = repeat_position + this.repeatLength() - 1;
 		   str += sequenceName + "\tminced:"+minced.VERSION+"\trepeat_unit\t" + repeat_position + "\t" + repeat_end + "\t1\t.\t.\tParent=" + parentName + ";ID=DR"+(m + 1) + "\n";
 	   }
 	   return str;

CRISPRFinder.java

@@ -291,7 +291,7 @@ private boolean findRepeats( DNASequence sequence, int readNum )
                 if(outputformat > 0) {
                 	String crispr_id = "CRISPR" + (++totalCrisprCount);
                 	out.print(sequence.getName() + "\tminced:" + minced.VERSION + "\tCRISPR\t");
-                    out.print((currCRISPR.start() + 1) + "\t" + (currCRISPR.end() + 2) + "\t");
+                    out.print((currCRISPR.start() + 1) + "\t" + (currCRISPR.end() + 1) + "\t");
                     out.print(currCRISPR.numRepeats() + "\t.\t.\tID="+ crispr_id);
                     out.print("\n");
                     if(outputformat == 2) {

minced.java

@@ -2,7 +2,7 @@
 
 public class minced
 {
-   public static final String VERSION = "0.1.5";
+   public static final String VERSION = "0.1.6";
 	public static void main(String[] args)
    {
       //default values