From 7c5a9c44448fe9dd2687a4743efb3ea8d62243d5 Mon Sep 17 00:00:00 2001
From: evantarbell <evan@dhcp205-217-240.wireless.buffalo.edu>
Date: Mon, 18 Feb 2019 18:12:35 -0500
Subject: [PATCH] bug fix for --score all option

---
 src/HMMR_ATAC/Main_HMMR_Driver.java | 23 ++++++++++++++++-------
 src/Node/TagNode.java               |  6 +++---
 2 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/src/HMMR_ATAC/Main_HMMR_Driver.java b/src/HMMR_ATAC/Main_HMMR_Driver.java
index 25f03dc..b683b00 100644
--- a/src/HMMR_ATAC/Main_HMMR_Driver.java
+++ b/src/HMMR_ATAC/Main_HMMR_Driver.java
@@ -72,7 +72,7 @@ public class Main_HMMR_Driver {
 	/*
 	 * Version number. Change as needed
 	 */
-	private static String versionNum = "1.2.3";
+	private static String versionNum = "1.2.4";
 	
 	@SuppressWarnings("unchecked")
 	public static void main(String[] args) throws IOException {
@@ -559,17 +559,26 @@ public static void main(String[] args) throws IOException {
 
 						}
 						ScoreNode scores = bedGraphMath.set(temp, overlaps);
+						double MAX = scores.getMax();
+						double MEAN = scores.getMean();
+						double MEDIAN = scores.getMedian();
+						double ZSCORE = (scores.getMean() - genomeMean)
+								/ genomeStd;
+						double FOLDCHANGE = scores.getMean() / genomeMean;
+						
 						if (scoreSys.equals("ave")) {
-							temp.setScore3(scores.getMean());
+							temp.setScore3(Double.toString(MEAN));
 						} else if (scoreSys.equals("fc")) {
-							temp.setScore3(scores.getMean() / genomeMean);
+							temp.setScore3(Double.toString(FOLDCHANGE));
 						} else if (scoreSys.equals("zscore")) {
-							temp.setScore3((scores.getMean() - genomeMean)
-									/ genomeStd);
+							temp.setScore3(Double.toString(ZSCORE));
 						} else if (scoreSys.equals("med")) {
-							temp.setScore3(scores.getMedian());
+							temp.setScore3(Double.toString(MEDIAN));
+						} else if (scoreSys.equals("all")){
+							String ANSWER = MAX+"_"+MEAN+"_"+MEDIAN+"_"+ZSCORE+"_"+FOLDCHANGE;
+							temp.setScore3(ANSWER);
 						} else {
-							temp.setScore3(scores.getMax());
+							temp.setScore3(Double.toString(MAX));
 						}
 						if ((int) temp.getScore2() == peak) {
 							temp = bedGraphMath.setSmooth(20, temp, overlaps);
diff --git a/src/Node/TagNode.java b/src/Node/TagNode.java
index e8a0373..1e7a811 100644
--- a/src/Node/TagNode.java
+++ b/src/Node/TagNode.java
@@ -12,7 +12,7 @@ public class TagNode {
 	private char strand = '\0';
 	private int Score = 0;
 	private double score2 = 0.0;
-	private double score3 = 0.0;
+	private String score3 = "";
 	private TagNode summit=null;
 	private TagNode upstream=null;
 	private TagNode downstream=null;
@@ -102,12 +102,12 @@ public void setSummit(TagNode t){
 	 * Set the third score variable
 	 * @param s a double representing a score
 	 */
-	public void setScore3(double s){score3 = s;}
+	public void setScore3(String s){score3 = s;}
 	/**
 	 * Access third score variable
 	 * @return a double representing a score
 	 */
-	public double getScore3(){return score3;}
+	public String getScore3(){return score3;}
 	/**
 	 * Set Score
 	 * @param score a double representing the entry's score