Added threshold option

src/HMMR_ATAC/ArgParser.java

@@ -58,6 +58,7 @@ public class ArgParser {
 		private boolean printExclude=false;
 		private boolean printTrain=true;
 		private long randomTrainSeed = 10151;
+		private double threshold = 30;
 
 		/**
 		 * Main constructor 
@@ -68,6 +69,11 @@ public ArgParser(String[] a,String ver){
 			version = ver;
 			set();
 		}
+		/**
+		 * Access the threshold for reporting peaks
+		 * @return a double to represent the threshold
+		 */
+		public double getThreshold(){return threshold;}
 		/**
 		 * Access the seed used for random sampling of training regions
 		 * @return a long to represent the seed for random sampling of training regions
@@ -465,6 +471,10 @@ private void set(){
 						randomTrainSeed=Long.parseLong(args[i+1]);
 						i++;
 						break;
+					case"threshold":
+						threshold = Double.parseDouble(args[i+1]);
+						i++;
+						break;
 					case"help":
 						printUsage();
 						//System.exit(0);
@@ -511,6 +521,7 @@ public void printUsage(){
 			System.out.println("\t--printExclude <true || false> Whether to output excluded regions into Output_exclude.bed. Default = false");
 			System.out.println("\t--printTrain <true || false> Whether to output training regions into Output_training.bed. Default = true");
 			System.out.println("\t--randomSeed <long> Seed to set for random sampling of training regions. Default is 10151");
+			System.out.println("\t--threshold <double> threshold for reporting peaks. Only peaks who's score is >= this value will be reported.");
 			System.out.println("\t-h , --help Print this help message and exit.");
 			System.exit(0);
 		}

src/HMMR_ATAC/BaumWelch.java

@@ -16,7 +16,6 @@
     You should have received a copy of the GNU General Public License
     along with this program.  If not, see <https://www.gnu.org/licenses/>.
  */
-
 import java.util.List;
 
 import JAHMMTest.BaumWelchScaledLearner;

src/HMMR_ATAC/Main_HMMR_Driver.java

@@ -89,6 +89,7 @@ public class Main_HMMR_Driver {
 	private static boolean printExclude = false;
 	private static boolean printTrain = true;
 	private static long randomTrainSeed=10151;
+	private static double threshold=0;
 
 	private static String trainingRegions;
 
@@ -129,6 +130,7 @@ public static void main(String[] args) throws IOException {
 		printExclude = p.getPrintExclude();
 		printTrain = p.getPrintTrain();
 		randomTrainSeed = p.getRandomTrainSeed();
+		threshold=p.getThreshold();
 //		printHMMRTracks = p.getPrintHMMRTracks(); 
 		//For run time calculation
 		Long startTime = System.currentTimeMillis();
@@ -654,7 +656,8 @@ public static void main(String[] args) throws IOException {
 					 * report the peaks and summits, if desired
 					 */
 					if (peaks && (int) temp.getScore2() == peak
-							&& temp.getLength() >= minLength) {
+							&& temp.getLength() >= minLength && 
+							Double.parseDouble(temp.getScore3()) >= threshold) {
 						if (temp.getSummit() != null) {
 							summits.println(temp.toString_ScoredSummit());
 						}