Bug-fix for BED files not containing strand information

Resolves #25 and extends bug-fix to GFF file manipulation. New default
behavior is to retain track header and anything that begins with ‘#’
character as unmodified in the output folder

Author: WilliamKMLai

src/scripts/Coordinate_Manipulation/BED_Manipulation/BEDtoGFF.java

@@ -17,8 +17,9 @@ public static void convertBEDtoGFF(File out_path, File input) throws IOException
 
 		while (scan.hasNextLine()) {
 			String[] temp = scan.nextLine().split("\t");
-			if(temp.length > 2) {
-				if(!temp[0].contains("track") && !temp[0].contains("#")) {
+			if(temp[0].toLowerCase().contains("track") || temp[0].startsWith("#")) { OUT.println(String.join("\t", temp)); }
+			else {
+				if(temp.length > 2) {
 					String name = temp[0] + "_" + temp[1] + "_" + temp[2]; //Get or make name from BED file
 					if(temp.length > 3) { name = temp[3]; }
 					String score = "0"; //Get or make direction

src/scripts/Coordinate_Manipulation/BED_Manipulation/ExpandBED.java

@@ -16,16 +16,17 @@ public static void expandBEDBorders(File out_path, File input, int SIZE, boolean
 
 		while (scan.hasNextLine()) {
 			String[] temp = scan.nextLine().split("\t");
-			if(temp.length > 2) {
-				if(!temp[0].contains("track") && !temp[0].contains("#")) {
+			if(temp[0].toLowerCase().contains("track") || temp[0].startsWith("#")) { OUT.println(String.join("\t", temp)); }
+			else {
+				if(temp.length > 2) {
 					if(Integer.parseInt(temp[1]) >= 0) {
 						//Default to add to border
 						int newstart = Integer.parseInt(temp[1]) - SIZE;
 						int newstop = Integer.parseInt(temp[2]) + SIZE;
 						if(ExCenter) { //Else expand from center
 							boolean EVEN = ((Integer.parseInt(temp[2]) - Integer.parseInt(temp[1])) % 2 == 0);
 				        	int CENTER = (int)((Integer.parseInt(temp[1]) + Integer.parseInt(temp[2])) / 2);
-				        	if(temp.length > 4) { if(!temp[5].equals("-") && !EVEN) { CENTER++; } }
+				        	if(temp.length > 5) { if(!temp[5].equals("-") && !EVEN) { CENTER++; } }
 					        newstart = CENTER - (SIZE / 2);
 					        newstop = CENTER + (SIZE / 2);
 				        }

src/scripts/Coordinate_Manipulation/GFF_Manipulation/ExpandGFF.java

@@ -19,8 +19,9 @@ public static void expandGFFBorders(File out_path, File input, int SIZE, boolean
 
 		while (scan.hasNextLine()) {
 			String[] temp = scan.nextLine().split("\t");
-			if(temp.length == 9) {
-				if(!temp[0].contains("track") && !temp[0].contains("#")) {
+			if(temp[0].toLowerCase().contains("track") || temp[0].startsWith("#")) { OUT.println(String.join("\t", temp)); }
+			else {
+				if(temp.length == 9) {
 					if(Integer.parseInt(temp[3]) >= 1) {
 						//Default to add to border
 						int newstart = Integer.parseInt(temp[3]) - SIZE;

src/scripts/Coordinate_Manipulation/GFF_Manipulation/GFFtoBED.java

@@ -19,8 +19,9 @@ public static void convertBEDtoGFF(File out_path, File input) throws IOException
 
 		while (scan.hasNextLine()) {
 			String[] temp = scan.nextLine().split("\t");
-			if(temp.length == 9) {
-				if(!temp[0].contains("track") && !temp[0].contains("#")) {
+			if(temp[0].toLowerCase().contains("track") || temp[0].startsWith("#")) { OUT.println(String.join("\t", temp)); }
+			else {
+				if(temp.length == 9) {
 					String name = temp[8];
 					String score = temp[5]; //Get or make direction
 					String dir = temp[6];