Fixed typos, and got rid of automatic extension correction

src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/SortBEDCLI.java

@@ -36,10 +36,10 @@ public class SortBEDCLI implements Callable<Integer> {
 
 	@Option(names = {"-o", "--output"}, description = "specify output file basename with no .cdt/.bed/.jtv extension (default=<bedFile>_SORT")
 	private String outputBasename = null;
-	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
-	private boolean gzOutput = false;
 	@Option(names = {"-c", "--center"}, description = "sort by center on the input size of expansion in bins (default=100)")
 	private int center = -999;
+	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
+	private boolean gzOutput = false;
 	@Option(names = {"-x", "--index"}, description = "sort by index from the specified start to the specified stop (0-indexed and half-open interval)",
 		arity = "2")
 	private int[] index = {-999, -999};

src/main/java/scriptmanager/cli/Peak_Analysis/RandomCoordinateCLI.java

@@ -30,7 +30,7 @@ public class RandomCoordinateCLI implements Callable<Integer> {
 	@Option(names = {"-o", "--output"}, description = "Specify output directory (default = current working directory), file name will be random_coordinates_<genomeName>_<window>bp.<ext>")
 	private File output = null;
 	@Option(names = {"-z", "--gzip"}, description = "output compressed output (default=false)")
-	private boolean zip = false;
+	private boolean gzOutput = false;
 	@Option(names = {"-f", "--gff"}, description = "file format output as GFF (default format as BED)")
 	private boolean formatIsBed = true;
 	@Option(names = {"-n", "--num-sites"}, description = "number of sites (default=1000)")
@@ -48,7 +48,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		RandomCoordinate.execute(genomeName, numSites, window, formatIsBed, output, zip); 
+		RandomCoordinate.execute(genomeName, numSites, window, formatIsBed, output, gzOutput); 
 
 		System.err.println( "Random Coordinate Generation Complete." );
 		return(0);

src/main/java/scriptmanager/cli/Peak_Analysis/TileGenomeCLI.java

@@ -30,7 +30,7 @@ public class TileGenomeCLI implements Callable<Integer> {
 	@Option(names = {"-o", "--output"}, description = "Specify output directory (default = current working directory), file name will be genome_tiles_<genomeName>_<window>bp.<ext>")
 	private File output = null;
 	@Option(names = {"-z", "--gzip"}, description = "output compressed output (default=false)")
-	private boolean zip = false;
+	private boolean gzOutput = false;
 	@Option(names = {"-f", "--gff"}, description = "file format output as GFF (default format as BED)")
 	private boolean formatIsBed = true;
 	@Option(names = {"-w", "--window"}, description = "window size in bp (default=200)")
@@ -46,7 +46,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		TileGenome.execute(genomeName, window, formatIsBed, output, zip);
+		TileGenome.execute(genomeName, window, formatIsBed, output, gzOutput);
 
 		System.err.println( "Genomic Tiling Complete." );
 		return(0);

src/main/java/scriptmanager/cli/Read_Analysis/AggregateDataCLI.java

@@ -13,7 +13,6 @@
 
 import scriptmanager.objects.ToolDescriptions;
 import scriptmanager.scripts.Read_Analysis.AggregateData;
-import scriptmanager.util.ExtensionFileFilter;
 
 /**
 	Read_AnalysisCLI/AggregateDataCLI
@@ -34,7 +33,7 @@ public class AggregateDataCLI implements Callable<Integer> {
 	@Option(names = {"-o", "--output"}, description = "Specify output file (default = <input1>_SCORES.out, <input2_SCORES.out, ... or ALL_SCORES.out if -m flag is used)")
 	private File output;
 	@Option(names = {"-z", "--gzip"}, description = "output compressed output (default=false)")
-	private boolean zip = false;
+	private boolean gzOutput = false;
 
 	@ArgGroup(exclusive = true, heading = "Aggregation Method%n")
 	AggType aggr = new AggType();
@@ -75,7 +74,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		AggregateData script_obj = new AggregateData(matFiles, output, merge, startROW, startCOL, aggType, zip);
+		AggregateData script_obj = new AggregateData(matFiles, output, merge, startROW, startCOL, aggType, gzOutput);
 		script_obj.run();
 
 		System.err.println(script_obj.getMessage());

src/main/java/scriptmanager/cli/Read_Analysis/ScaleMatrixCLI.java

@@ -30,7 +30,7 @@ public class ScaleMatrixCLI implements Callable<Integer> {
 	@Option(names = {"-o", "--output"}, description = "Specify output file (default = <matrixFilename>_SCALE.tab)")
 	private File output = null;
 	@Option(names = {"-z", "--gzip"}, description = "output compressed output (default=false)")
-	private boolean zip = false;
+	private boolean gzOutput = false;
 	@Option(names = {"-s", "--scaling-factor"}, description = "scaling factor (default=1)")
 	private double scale = 1;
 	@Option(names = {"-r", "--start-row"}, description = "")
@@ -49,7 +49,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}		
 
-		ScaleMatrix script_obj = new ScaleMatrix(matrixFile, output, scale, startROW, startCOL, zip);
+		ScaleMatrix script_obj = new ScaleMatrix(matrixFile, output, scale, startROW, startCOL, gzOutput);
 		script_obj.run();
 
 		System.err.println("All Matrices Scaled.");

src/main/java/scriptmanager/cli/Read_Analysis/TagPileupCLI.java

@@ -50,7 +50,7 @@ static class OutputOptions{
 			arity="0..1")
 		private ArrayList<String> outputMatrix = new ArrayList<String>(Arrays.asList("no","matrix","output"));
 		@Option(names = {"-z", "--gzip"}, description = "output compressed output (default=false)")
-		private boolean zip = false;
+		private boolean gzOutput = false;
 		@Option(names = {"--cdt"}, description = "output matrix in cdt format (default)")
 		private boolean cdt = false;
 		@Option(names = {"--tab"}, description = "output matrix in tab format")
@@ -286,7 +286,7 @@ private String validateInput() throws IOException {
 		p.setStandard(calcOptions.tagsEqual);
 
 		//Set output statuses
-		p.setGZIPstatus(outputOptions.zip);
+		p.setGZIPstatus(outputOptions.gzOutput);
 
 		//Set Ratio (code to standardize tags sequenced to genome size (1 tag / 1 bp))
 		if( p.getStandard() && filterOptions.blacklistFilter!=null ){

src/main/java/scriptmanager/cli/Sequence_Analysis/DNAShapefromBEDCLI.java

@@ -37,7 +37,7 @@ public class DNAShapefromBEDCLI implements Callable<Integer> {
 			"--output" }, description = "Specify basename for output files, files for each shape indicated will share this name with a different suffix")
 	private String outputBasename = null;
 	@Option(names = {"-z", "--gzip"}, description = "output compressed output (default=false)")
-	private boolean zip = false;
+	private boolean gzOutput = false;
 	@Option(names = { "--avg-composite" }, description = "Save average composite")
 	private boolean avgComposite = false;
 	@Option(names = { "-n", "--no-force" }, description = "don't force-strandedness (default is to force strandedness)")
@@ -76,7 +76,7 @@ public Integer call() throws Exception {
 		try {
 			// Generate Composite Plot
 			DNAShapefromBED script_obj = new DNAShapefromBED(genomeFASTA, bedFile, outputBasename, OUTPUT_TYPE,
-					forceStrand, new PrintStream[] { null, null, null, null }, zip);
+					forceStrand, new PrintStream[] { null, null, null, null }, gzOutput);
 			script_obj.run();
 
 			if (avgComposite) {

src/main/java/scriptmanager/cli/Sequence_Analysis/DNAShapefromFASTACLI.java

@@ -37,7 +37,7 @@ public class DNAShapefromFASTACLI implements Callable<Integer> {
 	@Option(names = { "--avg-composite" }, description = "Save average composite")
 	private boolean avgComposite = false;
 	@Option(names = {"-z", "--gzip"}, description = "output compressed output (default=false)")
-	private boolean zip = false;
+	private boolean gzOutput = false;
 
 	@ArgGroup(validate = false, heading = "Shape Options%n")
 	ShapeType shape = new ShapeType();
@@ -70,7 +70,7 @@ public Integer call() throws Exception {
 
 		// Generate Composite Plot
 		DNAShapefromFASTA script_obj = new DNAShapefromFASTA(fastaFile, outputBasename, OUTPUT_TYPE,
-				new PrintStream[] { null, null, null, null }, zip);
+				new PrintStream[] { null, null, null, null }, gzOutput);
 		script_obj.run();
 
 		// Print Composite Scores

src/main/java/scriptmanager/cli/Sequence_Analysis/RandomizeFASTACLI.java

@@ -34,7 +34,7 @@ public class RandomizeFASTACLI implements Callable<Integer> {
 	@Option(names = {"-s", "--seed"}, description = "specify an integer seed for reproducible outputs")
 	private Integer seed = null;
 	@Option(names = {"-z", "--gzip"}, description = "output compressed output (default=false)")
-	private boolean zip = false;
+	private boolean gzOutput = false;
 
 	@Override
 	public Integer call() throws Exception {
@@ -46,7 +46,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		RandomizeFASTA.randomizeFASTA(fastaFile, output, seed, zip);
+		RandomizeFASTA.randomizeFASTA(fastaFile, output, seed, gzOutput);
 
 		System.err.println("Randomization Complete.");
 		return (0);

src/main/java/scriptmanager/scripts/BAM_Format_Converter/BAMtoBED.java

@@ -100,9 +100,9 @@ public void run() throws IOException, InterruptedException {
 			}
 
 			if (OUTPUT_GZIP){
-				printPS("Output Gzip: yes");
-			} else{
-				printPS("Output Gzip: no");
+				printPS("Output GZip: yes");
+			} else {
+				printPS("Output GZip: no");
 			}
 
 			// Build&Print Header

src/main/java/scriptmanager/scripts/BAM_Format_Converter/BAMtoGFF.java

@@ -100,9 +100,9 @@ public void run() throws IOException, InterruptedException {
 			}
 
 			if (OUTPUT_GZIP){
-				printPS("Output Gzip: yes");
-			} else{
-				printPS("Output Gzip: no");
+				printPS("Output GZip: yes");
+			} else {
+				printPS("Output GZip: no");
 			}
 
 			// Build&Print Header

src/main/java/scriptmanager/scripts/BAM_Format_Converter/BAMtobedGraph.java

@@ -64,11 +64,12 @@ public void run() throws IOException, InterruptedException {
 		// Open Output File
 		if (OUTBASENAME != null) {
 			try {
+				String SUFFIX = ".bedGraph" + (OUTPUT_GZIP? ".gz": "");
 				if (STRAND <= 2) {
-					OUTF = GZipUtilities.makePrintStream(new File(OUTBASENAME + "_forward.bedGraph"), OUTPUT_GZIP);
-					OUTR = GZipUtilities.makePrintStream(new File(OUTBASENAME + "_reverse.bedGraph") , OUTPUT_GZIP);
+					OUTF = GZipUtilities.makePrintStream(new File(OUTBASENAME + "_forward" + SUFFIX), OUTPUT_GZIP);
+					OUTR = GZipUtilities.makePrintStream(new File(OUTBASENAME + "_reverse" + SUFFIX) , OUTPUT_GZIP);
 				} else {
-					OUTF = GZipUtilities.makePrintStream(new File(OUTBASENAME + "_midpoint.bedGraph"), OUTPUT_GZIP);
+					OUTF = GZipUtilities.makePrintStream(new File(OUTBASENAME + "_midpoint" + SUFFIX), OUTPUT_GZIP);
 				}
 			} catch (FileNotFoundException e) {
 				e.printStackTrace();
@@ -109,9 +110,9 @@ public void run() throws IOException, InterruptedException {
 			}
 
 			if (OUTPUT_GZIP){
-				printPS("Output Gzip: yes");
-			} else{
-				printPS("Output Gzip: no");
+				printPS("Output GZip: yes");
+			} else {
+				printPS("Output GZip: no");
 			}
 
 			// Print Header

src/main/java/scriptmanager/scripts/BAM_Format_Converter/BAMtoscIDX.java

@@ -104,9 +104,9 @@ public void run() throws IOException, InterruptedException {
 			}
 
 			if (OUTPUT_GZIP){
-				printPS("Output Gzip: yes");
-			} else{
-				printPS("Output Gzip: no");
+				printPS("Output GZip: yes");
+			} else {
+				printPS("Output GZip: no");
 			}
 
 			// Print Header

src/main/java/scriptmanager/scripts/Coordinate_Manipulation/BED_Manipulation/SortBED.java

@@ -1,18 +1,21 @@
 package scriptmanager.scripts.Coordinate_Manipulation.BED_Manipulation;
 
+import java.io.BufferedOutputStream;
 import java.io.BufferedReader;
 import java.io.File;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
+import java.util.zip.GZIPOutputStream;
 
 import scriptmanager.objects.CoordinateObjects.BEDCoord;
 import scriptmanager.util.GZipUtilities;
 
 /**
- * This class contains scripts for sorting coordinate intervals (BED/GFF) by the tag counts of a CDT matrix file.
+ * Sort coordinate intervals (BED) by the tag counts of a CDT matrix file.
  *
  * @author William KM Lai
  * @see scriptmanager.cli.Coordinate_Manipulation.BED_Manipulation.SortBEDCLI
@@ -28,7 +31,7 @@ public class SortBED {
 	 * @param START_INDEX the start column to consider when summing values to sort
 	 * @param STOP_INDEX
 	 * @param gzOutput if true, the output files will be gzipped.
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	public static void sortBEDbyCDT(String outbase, File bed, File cdt, int START_INDEX, int STOP_INDEX, boolean gzOutput ) throws IOException {
 		ArrayList<BEDCoord> SORT = new ArrayList<BEDCoord>();
@@ -38,7 +41,7 @@ public static void sortBEDbyCDT(String outbase, File bed, File cdt, int START_IN
 		BufferedReader br = GZipUtilities.makeReader(cdt);
 		// Initialize line variable to loop through
 		String line = br.readLine();
-		while ((line = br.readLine()) != null) {
+		while (line != null) {
 			String[] ID = line.split("\t");
 			if (!ID[0].contains("YORF") && !ID[0].contains("NAME")) {
 				double count = 0;
@@ -50,14 +53,19 @@ public static void sortBEDbyCDT(String outbase, File bed, File cdt, int START_IN
 			} else {
 				CDTHeader = line;
 			}
+			line = br.readLine();
 		}
 		br.close();
 		// Sort by score
 		Collections.sort(SORT, BEDCoord.ScoreComparator);
 
 		PrintStream OUT;
 		// Initialize output writer
-		OUT = GZipUtilities.makePrintStream(new File(outbase + ".cdt"), gzOutput);
+		if (gzOutput) {
+			OUT = new PrintStream(new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(outbase + ".cdt.gz"))));
+		} else {
+			OUT = new PrintStream(new BufferedOutputStream(new FileOutputStream(outbase + ".cdt")));
+		}
 		// Output sorted CDT File
 		OUT.println(CDTHeader);
 		for (int x = 0; x < SORT.size(); x++) {
@@ -73,7 +81,7 @@ public static void sortBEDbyCDT(String outbase, File bed, File cdt, int START_IN
 		br = GZipUtilities.makeReader(bed);
 		// Initialize line variable to loop through
 		line = br.readLine();
-		while ((line = br.readLine()) != null) {
+		while (line != null) {
 			String ID = line.split("\t")[3];
 			if (!ID.contains("YORF") && !ID.contains("NAME")) {
 				BEDFile.put(ID, line);
@@ -83,11 +91,15 @@ public static void sortBEDbyCDT(String outbase, File bed, File cdt, int START_IN
 		br.close();
 
 		// Initialize output writer
-		OUT = GZipUtilities.makePrintStream(new File(outbase + ".bed"), gzOutput);
+		if (gzOutput) {
+			OUT = new PrintStream(new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(outbase + ".bed.gz"))));
+		} else {
+			OUT = new PrintStream(new BufferedOutputStream(new FileOutputStream(outbase + ".bed")));
+		}
 		// Output sorted BED File
 		for (int x = 0; x < SORT.size(); x++) {
 			OUT.println(BEDFile.get(SORT.get(x).getName()));
 		}
 		OUT.close();
 	}
-}
+}

src/main/java/scriptmanager/scripts/Coordinate_Manipulation/GFF_Manipulation/SortGFF.java

@@ -40,7 +40,8 @@ public static void sortGFFbyCDT(String outname, File gff, File cdt, int START_IN
 		Collections.sort(SORT, GFFCoord.ScoreComparator);
 
 		// Output sorted CDT File
-		PrintStream OUT = GZipUtilities.makePrintStream(new File(outname + ".cdt"), gzOutput);
+		String SUFFIX = ".cdt" + (gzOutput? ".gz": "");
+		PrintStream OUT = GZipUtilities.makePrintStream(new File(outname + SUFFIX), gzOutput);
 		OUT.println(CDTHeader);
 		for (int x = 0; x < SORT.size(); x++) {
 			OUT.println(CDTFile.get(SORT.get(x).getName()));
@@ -64,7 +65,8 @@ public static void sortGFFbyCDT(String outname, File gff, File cdt, int START_IN
 		br.close();
 
 		// Output sorted GFF File
-		OUT = GZipUtilities.makePrintStream(new File(outname + ".gff"), gzOutput);
+		SUFFIX = ".gff" + (gzOutput? ".gz": "");
+		OUT = GZipUtilities.makePrintStream(new File(outname + SUFFIX), gzOutput);
 		for (int x = 0; x < SORT.size(); x++) {
 			OUT.println(GFFFile.get(SORT.get(x).getName()));
 		}

src/main/java/scriptmanager/window_interface/BAM_Format_Converter/BAMtoBEDWindow.java

@@ -268,7 +268,7 @@ public void itemStateChanged(ItemEvent e) {
 		sl_contentPane.putConstraint(SpringLayout.EAST, btnOutputDirectory, -250, SpringLayout.EAST, contentPane);
 		contentPane.add(btnOutputDirectory);
 
-		chckbxGzipOutput = new JCheckBox("Output Gzip");
+		chckbxGzipOutput = new JCheckBox("Output GZip");
 		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnIndex);
 		sl_contentPane.putConstraint(SpringLayout.EAST, chckbxGzipOutput, -83, SpringLayout.WEST, btnOutputDirectory);
 		contentPane.add(chckbxGzipOutput);

src/main/java/scriptmanager/window_interface/BAM_Format_Converter/BAMtoGFFWindow.java

@@ -268,7 +268,7 @@ public void itemStateChanged(ItemEvent e) {
 		sl_contentPane.putConstraint(SpringLayout.EAST, btnOutputDirectory, -250, SpringLayout.EAST, contentPane);
 		contentPane.add(btnOutputDirectory);
 
-		chckbxGzipOutput = new JCheckBox("Output Gzip");
+		chckbxGzipOutput = new JCheckBox("Output GZip");
 		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnIndex);
 		sl_contentPane.putConstraint(SpringLayout.EAST, chckbxGzipOutput, -83, SpringLayout.WEST, btnOutputDirectory);
 		contentPane.add(chckbxGzipOutput);

src/main/java/scriptmanager/window_interface/BAM_Format_Converter/BAMtobedGraphWindow.java

@@ -250,7 +250,7 @@ public void itemStateChanged(ItemEvent e) {
 		sl_contentPane.putConstraint(SpringLayout.EAST, btnOutputDirectory, -250, SpringLayout.EAST, contentPane);
 		contentPane.add(btnOutputDirectory);
 
-		chckbxGzipOutput = new JCheckBox("Output Gzip");
+		chckbxGzipOutput = new JCheckBox("Output GZip");
 		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnIndex);
 		sl_contentPane.putConstraint(SpringLayout.EAST, chckbxGzipOutput, -83, SpringLayout.WEST, btnOutputDirectory);
 		contentPane.add(chckbxGzipOutput);

src/main/java/scriptmanager/window_interface/BAM_Format_Converter/BAMtoscIDXWindow.java

@@ -250,7 +250,7 @@ public void itemStateChanged(ItemEvent e) {
 		sl_contentPane.putConstraint(SpringLayout.EAST, btnOutputDirectory, -250, SpringLayout.EAST, contentPane);
 		contentPane.add(btnOutputDirectory);
 
-		chckbxGzipOutput = new JCheckBox("Output Gzip");
+		chckbxGzipOutput = new JCheckBox("Output GZip");
 		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnIndex);
 		sl_contentPane.putConstraint(SpringLayout.EAST, chckbxGzipOutput, -83, SpringLayout.WEST, btnOutputDirectory);
 		contentPane.add(chckbxGzipOutput);

src/main/java/scriptmanager/window_interface/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFWindow.java

@@ -201,7 +201,7 @@ public void actionPerformed(ActionEvent e) {
 		contentPane.add(btnOutput);
 		btnConvert.addActionListener(this);
 
-		chckbxGzipOutput = new JCheckBox("Output GZIP");
+		chckbxGzipOutput = new JCheckBox("Output GZip");
 		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnConvert);
 		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxGzipOutput, 36, SpringLayout.WEST, contentPane);
 		contentPane.add(chckbxGzipOutput);

src/main/java/scriptmanager/window_interface/Coordinate_Manipulation/BED_Manipulation/ExpandBEDWindow.java

@@ -203,7 +203,7 @@ public void actionPerformed(ActionEvent e) {
 		});
 		contentPane.add(btnOutput);
 
-		chckbxGzipOutput = new JCheckBox("Output GZIP");
+		chckbxGzipOutput = new JCheckBox("Output GZip");
 		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnOutput);
 		sl_contentPane.putConstraint(SpringLayout.EAST, chckbxGzipOutput, -10, SpringLayout.EAST, contentPane);
 		contentPane.add(chckbxGzipOutput);