add hg38 to TileGenome and RandCoord

Address issue ticket #80 by adding `hg38` and `hg38_contigs` genome options to TileGenome and RandomCoordinate tools

util.GenomeSizeReference
- update initialize options to include both versions of hg38
- add JavaDocs comments
scripts.RandomCoordinate
- turn script into a public static void method
- add JavaDocs comments
scripts.TileGenome
- turn script into a public static void method
- add JavaDocs comments
window_interface.RandomCoordinateWindow
- add hg38 as selection options
- adjust script call to use public static method
- add JavaDocs comments
window_interface.TileGenomeWindow
- add hg38 as selection options
- adjust script call to use public static method
- add JavaDocs comments
cli.RandomCoordinateCLI
- add hg38 as selection options in help message of Parameter
- adjust script call to use public static method
- add JavaDocs comments
cli.TileGenomeCLI
- add hg38 as selection options in help message of Parameter
- adjust script call to use public static method
- add JavaDocs comments

Author: owlang

src/cli/Peak_Analysis/RandomCoordinateCLI.java

@@ -24,7 +24,7 @@
 	exitCodeOnExecutionException = 1)
 public class RandomCoordinateCLI implements Callable<Integer> {
 
-	@Parameters( index = "0", description = "reference genome [sacCer3|sacCer3_cegr|hg19|hg19_contigs|mm10]")
+	@Parameters( index = "0", description = "reference genome [sacCer3|sacCer3_cegr|hg38|hg38_contigs|hg19|hg19_contigs|mm10]")
 	private String genomeName;
 
 	@Option(names = {"-o", "--output"}, description = "Specify output directory (default = current working directory), file name will be random_coordinates_<genomeName>_<window>bp.<ext>")
@@ -46,8 +46,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		RandomCoordinate script_obj = new RandomCoordinate(genomeName, numSites, window, formatIsBed, output); 
-		script_obj.execute();
+		RandomCoordinate.execute(genomeName, numSites, window, formatIsBed, output); 
 
 		System.err.println( "Random Coordinate Generation Complete." );
 		return(0);

src/cli/Peak_Analysis/TileGenomeCLI.java

@@ -24,7 +24,7 @@
 	exitCodeOnExecutionException = 1)
 public class TileGenomeCLI implements Callable<Integer> {
 
-	@Parameters( index = "0", description = "reference genome [sacCer3|sacCer3_cegr|hg19|hg19_contigs|mm10]")
+	@Parameters( index = "0", description = "reference genome [sacCer3|sacCer3_cegr|hg38|hg38_contigs|hg19|hg19_contigs|mm10]")
 	private String genomeName;
 
 	@Option(names = {"-o", "--output"}, description = "Specify output directory (default = current working directory), file name will be genome_tiles_<genomeName>_<window>bp.<ext>")
@@ -44,8 +44,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		TileGenome script_obj = new TileGenome(genomeName, window, formatIsBed, output);
-		script_obj.execute();
+		TileGenome.execute(genomeName, window, formatIsBed, output);
 
 		System.err.println( "Genomic Tiling Complete." );
 		return(0);

src/scripts/Peak_Analysis/RandomCoordinate.java

@@ -11,35 +11,45 @@
 import objects.CoordinateObjects.GenericCoord;
 import util.GenomeSizeReference;
 
+/**
+ * Class with static method for creating a coordinate file of random sites across a genome.
+ * 
+ * @author William KM Lai
+ * @see util.GenomeSizeReference
+ */
 public class RandomCoordinate {
-	private File OUTPUT = null;
-	private String GENOME = "";
-	private int numSites = 0;
-	private int windowSize = 0;
-	
-	private boolean BEDout = true;
-	private String EXTENSION = ".bed";
-	
-	public RandomCoordinate(String gen, int sites, int size, boolean bed, File out) {
-		GENOME = gen;
-		numSites = sites;
-		windowSize = size;
-		OUTPUT = out;
-		BEDout = bed;
-		if(BEDout) { EXTENSION = ".bed"; }
-		else { EXTENSION = ".gff"; }
-	}
-	
-	public void execute() throws IOException, IllegalArgumentException {
-	    GenomeSizeReference coord = new GenomeSizeReference(GENOME);
+	/**
+	 * Create and write output BED/GFF file of random genomic intervals for a genome
+	 * build. All entries will be "+" stranded, score="0.0", and the identifier
+	 * column is a genomic coordinate string (\<chr\>_\<start\>_\<stop\>_\<dir\>).
+	 * For the BED format, the identifier column will be the 4th column while the
+	 * GFF format will use the 9th column for the identifier.
+	 * 
+	 * @param GENOME     the String encoding the genome build to tile (matches util.GenomeSizeReference)
+	 * @param numSites   the number of random coordinate sites to sample
+	 * @param windowSize the base-pair length of each coordinate interval
+	 * @param BEDout     coordinate file format of output where BED-format is used if true and GFF-format used if false
+	 * @param OUTPUT     the file to write the coordinate tile output to (if null, a default filename is determined using \<GENOME\>_\<numSites\>SITES_\<windowSize\>bp.\<ext\>)
+	 * @throws IOException
+	 * @throws IllegalArgumentException
+	 */
+	public static void execute(String GENOME, int numSites, int windowSize, boolean BEDout, File OUTPUT) throws IOException, IllegalArgumentException {
+		GenomeSizeReference coord = new GenomeSizeReference(GENOME);
 	    if(!coord.isSmaller(windowSize)) {
 	    	System.err.println("Window size is too large for selected genome!!!\n");
 	    	JOptionPane.showMessageDialog(null, "Invalid Window Size Entered!!!");
 	    } else {
+	    	String EXTENSION = ".gff";
+			if (BEDout) {
+				EXTENSION = ".bed";
+			}
 		    String randomName = GENOME + "_" + numSites + "SITES_" + windowSize + "bp" + EXTENSION;
 		    PrintStream OUT = null;
-		    if(OUTPUT == null) OUT = new PrintStream(randomName);
-		    else OUT = new PrintStream(OUTPUT);
+			if (OUTPUT == null) {
+				OUT = new PrintStream(randomName);
+			} else {
+				OUT = new PrintStream(OUTPUT);
+			}
 		    for(int x = 0; x < numSites; x++) {
 		    	GenericCoord temp = coord.generateRandomCoord(windowSize);
 		    	if(BEDout) {

src/scripts/Peak_Analysis/TileGenome.java

@@ -7,31 +7,42 @@
 import objects.CoordinateObjects.GFFCoord;
 import util.GenomeSizeReference;
 
-public class TileGenome {
-	private File OUTPUT = null;
-	private String GENOME = "";
-	private long windowSize = 0;
-	
-	private boolean BEDout = true;
-	private String EXTENSION = ".bed";
-	
-	public TileGenome(String gen, int size, boolean bed, File out) {
-		GENOME = gen;
-		windowSize = size;
-		OUTPUT = out;
-		BEDout = bed;
-		if(BEDout) { EXTENSION = ".bed"; }
-		else { EXTENSION = ".gff"; }
-	}
-	
-	public void execute() throws IOException, IllegalArgumentException {
-	    GenomeSizeReference coord = new GenomeSizeReference(GENOME);
-	    
-	    String fileName = GENOME + "_" + windowSize + "bp" + EXTENSION;
+/**
+ * Class with static method for creating a coordinate file of tiles across a genome.
+ * 
+ * @author William KM Lai
+ * @see util.GenomeSizeReference
+ */
+	public class TileGenome {
+
+	/**
+	 * Create and write output BED/GFF file of genomic intervals tiling the genome.
+	 * All entries will be "+" stranded, score="0.0", and the identifier column is a
+	 * genomic coordinate string (\<chr\>_\<start\>_\<stop\>_\<dir\>). For the BED format,
+	 * the identifier column will be the 4th column while the GFF format will use
+	 * the 9th column for the identifier.
+	 * 
+	 * @param GENOME     the String encoding the genome build to tile (matches util.GenomeSizeReference)
+	 * @param windowSize the base-pair length of the tiles
+	 * @param BEDout     coordinate file format of output where BED-format is used if true and GFF-format used if false
+	 * @param OUTPUT     the file to write the coordinate tile output to (if null, a default filename is determined using \<GENOME\>_\<windowSize\>bp.\<ext\>)
+	 * @throws IOException
+	 * @throws IllegalArgumentException
+	 */
+	public static void execute(String GENOME, int windowSize, boolean BEDout, File OUTPUT) throws IOException, IllegalArgumentException {
+		GenomeSizeReference coord = new GenomeSizeReference(GENOME);
+		String EXTENSION = ".gff";
+		if (BEDout) {
+			EXTENSION = ".bed";
+		}
+		String fileName = GENOME + "_" + windowSize + "bp" + EXTENSION;
 		PrintStream OUT = null;
-		if(OUTPUT == null) OUT = new PrintStream(new File(fileName));
-	    else OUT = new PrintStream(OUTPUT);
-		
+		if (OUTPUT == null) {
+			OUT = new PrintStream(new File(fileName));
+		} else {
+			OUT = new PrintStream(OUTPUT);
+		}
+
 		for(int x = 0; x < coord.getChrom().size(); x++) {
 			String CHROM = coord.getChrom().get(x);
 			long SIZE = coord.getChromSize().get(x);