create BEDtoGFF command line version

This tool did not implement JFrame elements in the script class so the
CLI implementation did not need to create an src/window_interface/*/
BEDtoGFFOutput class. As a result, fewer files were affected:

window_interface/*Window
	-adjust output argument when initializing script class to be
		full filename and not just directory
script/*
	-use output as filename rather than directory name
	-add capability to  print to STDOUT
cli/*
	-call appropriate script class
	-write up picocli parsing objects
	-write up validateInput() method to check inputs and write
		messages for the user

Author: owlang

src/cli/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFCLI.java

@@ -12,7 +12,7 @@
 
 import objects.ToolDescriptions;
 import util.ExtensionFileFilter;
-//import scripts.Coordinate_Manipulation.BED_Manipulation.BEDtoGFF;
+import scripts.Coordinate_Manipulation.BED_Manipulation.BEDtoGFF;
 
 /**
 	Coordinate_ManipulationCLI/BEDtoGFFCLI
@@ -24,6 +24,14 @@
 	exitCodeOnExecutionException = 1)
 public class BEDtoGFFCLI implements Callable<Integer> {
 
+	@Parameters( index = "0", description = "the BED file to convert")
+	private File bedFile;
+	
+	@Option(names = {"-o", "--output"}, description = "specify output directory (name will be same as original with .gff ext)")
+	private File output = null;
+	@Option(names = {"-s", "--stdout"}, description = "output gff to STDOUT")
+	private boolean stdout = false;
+	
 	@Override
 	public Integer call() throws Exception {
 		System.err.println( ">BEDtoGFFCLI.call()" );
@@ -34,16 +42,46 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		//SEStats.getSEStats( output, bamFile, null );
+		BEDtoGFF.convertBEDtoGFF(output, bedFile);
 
-		//System.err.println("Calculations Complete");
+		System.err.println("Conversion Complete");
 		return(0);
 	}
 
 	private String validateInput() throws IOException {
 		String r = "";
-		//validate input here
-		//append messages to the user to `r`
+		
+		//check inputs exist
+		if(!bedFile.exists()){
+			r += "(!)BED file does not exist: " + bedFile.getName() + "\n";
+			return(r);
+		}
+		//check input extensions
+		if(!"bed".equals(ExtensionFileFilter.getExtension(bedFile))){
+			r += "(!)Is this a BED file? Check extension: " + bedFile.getName() + "\n";
+		}
+		//set default output filename
+		if(output==null && !stdout){
+			output = new File(ExtensionFileFilter.stripExtension(bedFile) + ".gff");
+		//check stdout and output not both selected
+		}else if(stdout){
+			if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }
+		//check output filename is valid
+		}else{
+			//check ext
+			try{
+				if(!"gff".equals(ExtensionFileFilter.getExtension(output))){
+					r += "(!)Use BED extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".bed\n";
+				}
+			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use BED extension for output filename. Try: " + output + ".youroutputextensionhere\n"; }
+			//check directory
+			if(output.getParent()==null){
+	// 			System.err.println("default to current directory");
+			} else if(!new File(output.getParent()).exists()){
+				r += "(!)Check output directory exists: " + output.getParent() + "\n";
+			}
+		}
+		
 		return(r);
 	}
 }

src/scripts/Coordinate_Manipulation/BED_Manipulation/BEDtoGFF.java

@@ -7,13 +7,12 @@
 import java.util.Scanner;
 
 public class BEDtoGFF {
-	public static void convertBEDtoGFF(File out_path, File input) throws IOException {
+	public static void convertBEDtoGFF(File out_filepath, File input) throws IOException {
 		//chr22  TeleGene enhancer  10000000  10001000  500 +  .  touch1
-	    String gffName = (input.getName()).substring(0,input.getName().length() - 4) + ".gff";
-	    Scanner scan = new Scanner(input);
-	    PrintStream OUT = null;
-	    if(out_path == null) OUT = new PrintStream(gffName);
-	    else OUT = new PrintStream(out_path + File.separator + gffName);
+		
+		Scanner scan = new Scanner(input);
+	    PrintStream OUT = System.out;
+	    if( out_filepath != null ) OUT = new PrintStream(out_filepath);
 
 		while (scan.hasNextLine()) {
 			String[] temp = scan.nextLine().split("\t");

src/window_interface/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFWindow.java

@@ -55,7 +55,14 @@ class Task extends SwingWorker<Void, Void> {
         public Void doInBackground() throws IOException {
         	setProgress(0);
         	for(int x = 0; x < BEDFiles.size(); x++) {
-				BEDtoGFF.convertBEDtoGFF(OUTPUT_PATH, BEDFiles.get(x));
+        		File XBED = BEDFiles.get(x);
+        		// Set outfilepath
+        		String gffName = (XBED.getName()).substring(0,XBED.getName().length() - 4) + ".gff";
+        		File OUT_FILE = null;
+        		if(OUTPUT_PATH == null) OUT_FILE = new File( gffName );
+        		else OUT_FILE = new File( OUTPUT_PATH + File.separator + gffName );
+        		// Execute conversion and update progress
+				BEDtoGFF.convertBEDtoGFF(OUTPUT_PATH, XBED);
 				int percentComplete = (int)(((double)(x + 1) / BEDFiles.size()) * 100);
         		setProgress(percentComplete);
         	}