Fixed typos

Author: benjaminbeer256

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