adding FeatureCounter

lib/FeatureCounter.groovy

@@ -0,0 +1,35 @@
+/* 
+ * Class for feature counter
+ *
+ * @authors
+ * Luca Cozzuto <lucacozzuto@gmail.com>
+ */
+
+ class FeatureCounter {
+
+	/*
+	 * Properties definition
+	 */
+
+     String input = ''
+     String output = ''
+     String annotation = ''
+     String memory = 0
+     String strand = ''
+     Integer cpus = 1
+     String extrapars = ''
+
+	/* 
+	 *  count feature with htseq-count
+ 	 */	
+
+    def public htseqCount() {
+
+    """
+		htseq-count ${this.extrapars} -s ${this.strand} -f bam ${this.input} ${this.annotation} > ${this.output}
+    """
+	}
+
+
+
+}

lib/NGSaligner.groovy

@@ -201,7 +201,7 @@
 
 
 	/*
-     * Get genome STATS from Bowtie index
+     * Get genome STATS from Bowtie2 index
      */ 
 
     def public genomeStatsFromBowtie2Index() {