Added gzip support to plain text tools addressing #91

src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoBEDCLI.java

@@ -40,6 +40,8 @@ public BAMtoBEDCLI(){}
 	private File output = null;
 	@Option(names = {"-s", "--stdout"}, description = "stream output file to STDOUT (cannot be used with \"-o\" flag)" )
 	private boolean stdout = false;
+	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
+	private boolean gzOutput = false;
 
 	//Read
 	@ArgGroup(exclusive = true, multiplicity = "0..1", heading = "%nSelect Read to output:%n\t@|fg(red) (select no more than one of these options)|@%n")
@@ -81,7 +83,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		BAMtoBED script_obj = new BAMtoBED(bamFile, output, STRAND, PAIR, MIN_INSERT, MAX_INSERT, null);
+		BAMtoBED script_obj = new BAMtoBED(bamFile, output, STRAND, PAIR, MIN_INSERT, MAX_INSERT, null, gzOutput);
 		script_obj.run();
 
 		System.err.println("Conversion Complete");
@@ -123,7 +125,7 @@ private String validateInput() throws IOException {
 		}else if(stdout){
 			if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }
 		//check output filename is valid
-		}else{
+		} else {
 			//check directory
 			if(output.getParent()==null){
 	// 			System.err.println("default to current directory");

src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoGFFCLI.java

@@ -40,6 +40,8 @@ public BAMtoGFFCLI(){}
 	private File output = null;
 	@Option(names = {"-s", "--stdout"}, description = "stream output file to STDOUT (cannot be used with \"-o\" flag)" )
 	private boolean stdout = false;
+	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
+	private boolean gzOutput = false;
 
 	//Read
 	@ArgGroup(exclusive = true, multiplicity = "0..1", heading = "%nSelect Read to output:%n\t@|fg(red) (select no more than one of these options)|@%n")
@@ -81,7 +83,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		BAMtoGFF script_obj = new BAMtoGFF(bamFile, output, STRAND, PAIR, MIN_INSERT, MAX_INSERT, null);
+		BAMtoGFF script_obj = new BAMtoGFF(bamFile, output, STRAND, PAIR, MIN_INSERT, MAX_INSERT, null, gzOutput);
 		script_obj.run();
 
 		System.err.println("Conversion Complete");

src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtobedGraphCLI.java

@@ -38,6 +38,9 @@ public BAMtobedGraphCLI(){}
 
 	@Option(names = {"-o", "--output"}, description = "specify output directory (name will be same as original with _<strand>.bedgraph ext)" )
 	private String outputBasename = null;
+
+	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
+	private boolean gzOutput = false;
 
 	//Read
 	@ArgGroup(exclusive = true, multiplicity = "0..1", heading = "%nSelect Read to output:%n\t@|fg(red) (select no more than one of these options)|@%n")
@@ -77,7 +80,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		BAMtobedGraph script_obj = new BAMtobedGraph(bamFile, outputBasename, STRAND, PAIR, MIN_INSERT, MAX_INSERT, null);
+		BAMtobedGraph script_obj = new BAMtobedGraph(bamFile, outputBasename, STRAND, PAIR, MIN_INSERT, MAX_INSERT, null, gzOutput);
 		script_obj.run();
 
 		System.err.println("Conversion Complete");

src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoscIDXCLI.java

@@ -40,7 +40,8 @@ public BAMtoscIDXCLI(){}
 	private File output = null;
 	@Option(names = {"-s", "--stdout"}, description = "stream output file to STDOUT (cannot be used with \"-o\" flag)" )
 	private boolean stdout = false;
-
+	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
+	private boolean gzOutput = false;
 	//Read
 	@ArgGroup(exclusive = true, multiplicity = "0..1", heading = "%nSelect Read to output:%n\t@|fg(red) (select no more than one of these options)|@%n")
 	ReadType readType = new ReadType();
@@ -78,8 +79,8 @@ public Integer call() throws Exception {
 			System.err.println("Invalid input. Check usage using '-h' or '--help'");
 			System.exit(1);
 		}
-		
-		BAMtoscIDX script_obj = new BAMtoscIDX(bamFile, output, STRAND, PAIR, MIN_INSERT, MAX_INSERT, null);
+
+		BAMtoscIDX script_obj = new BAMtoscIDX(bamFile, output, STRAND, PAIR, MIN_INSERT, MAX_INSERT, null, gzOutput);
 		script_obj.run();
 
 		System.err.println("Conversion Complete");
@@ -120,7 +121,7 @@ private String validateInput() throws IOException {
 		}else if(stdout){
 			if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }
 		//check output filename is valid
-		}else{
+		} else {
 			//check directory
 			if(output.getParent()==null){
 	// 			System.err.println("default to current directory");

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

@@ -71,7 +71,7 @@ private String validateInput() throws IOException {
 		}
 		//set default output filename
 		if(output==null && !stdout){
-			String NAME = ExtensionFileFilter.stripExtension(bedFile) + ".gff";
+			String NAME = ExtensionFileFilter.stripExtensionIgnoreGZ(bedFile) + ".gff";
 			NAME += gzOutput ? ".gz" : "";
 			output = new File(NAME);
 		//check stdout and output not both selected

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

@@ -111,7 +111,6 @@ private String validateInput() throws IOException {
 			if (!stdout) {
 				String NAME = ExtensionFileFilter.stripExtension(bedFile);
 				NAME += byCenter ? "_" + Integer.toString(SIZE) + "bp.bed" : "_border_" + Integer.toString(SIZE) + "bp.bed";
-				NAME += gzOutput ? ".gz" : "";
 				output = new File(NAME);
 			//check stdout and output not both selected
 			} else {

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

@@ -93,7 +93,7 @@ private String validateInput() throws IOException {
 
 		//set default output filename
 		if(outputBasename==null){
-			outputBasename = ExtensionFileFilter.stripExtension(bedFile) + "_SORT";
+			outputBasename = ExtensionFileFilter.stripExtensionIgnoreGZ(bedFile) + "_SORT";
 		//check output filename is valid
 		}else{
 			//no extension check

src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFCLI.java

@@ -38,8 +38,10 @@ public ExpandGFFCLI(){}
 
 	@Option(names = {"-o", "--output"}, description = "specify output filename (name will be same as original with coordinate info appended)")
 	private File output = null;
-	@Option(names = {"-s", "--stdout"}, description = "output bed to STDOUT")
+	@Option(names = {"-s", "--stdout"}, description = "output gff to STDOUT")
 	private boolean stdout = false;
+	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
+	private boolean gzOutput = false;
 
 	@ArgGroup(validate = false, heading = "%nType of Expansion%n")
 	ExpandType expandType = new ExpandType();
@@ -67,7 +69,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		ExpandGFF.expandGFFBorders(output, gffFile, SIZE, byCenter);
+		ExpandGFF.expandGFFBorders(output, gffFile, SIZE, byCenter, gzOutput);
 
 		System.err.println("Expansion Complete");
 		return(0);
@@ -82,7 +84,7 @@ private String validateInput() throws IOException {
 			return(r);
 		}
 		//check input extensions
-		if(!"gff".equals(ExtensionFileFilter.getExtension(gffFile))){
+		if(!"gff".equals(ExtensionFileFilter.getExtensionIgnoreGZ(gffFile))){
 			r += "(!)Is this a GFF file? Check extension: " + gffFile.getName() + "\n";
 		}
 

src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDCLI.java

@@ -34,6 +34,8 @@ public class GFFtoBEDCLI implements Callable<Integer> {
 	private File output = null;
 	@Option(names = {"-s", "--stdout"}, description = "output bed to STDOUT")
 	private boolean stdout = false;
+	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
+	private boolean gzOutput = false;
 
 	/**
 	 * Runs when this subcommand is called, running script in respective script package with user defined arguments
@@ -49,7 +51,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		GFFtoBED.convertGFFtoBED(output, gffFile);
+		GFFtoBED.convertGFFtoBED(output, gffFile, gzOutput);
 
 		System.err.println("Conversion Complete");
 		return(0);
@@ -65,7 +67,7 @@ private String validateInput() throws IOException {
 		}
 		//set default output filename
 		if(output==null && !stdout){
-			output = new File(ExtensionFileFilter.stripExtension(gffFile) + ".bed");
+			output = new File(ExtensionFileFilter.stripExtensionIgnoreGZ(gffFile) + ".bed");
 		//check stdout and output not both selected
 		}else if(stdout){
 			if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }

src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/SortGFFCLI.java

@@ -36,6 +36,8 @@ public class SortGFFCLI implements Callable<Integer> {
 
 	@Option(names = {"-o", "--output"}, description = "specify output file basename with no .cdt/.gff/.jtv extension (default=<gffFile>_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 = {"-x", "--index"}, description = "sort by index from the specified start to the specified stop (0-indexed and half-open interval)",
@@ -64,7 +66,7 @@ public Integer call() throws Exception {
 			index[1] = (CDT_SIZE / 2) + (center / 2);
 		}
 
-		SortGFF.sortGFFbyCDT(outputBasename, gffFile, cdtFile, index[0], index[1]);
+		SortGFF.sortGFFbyCDT(outputBasename, gffFile, cdtFile, index[0], index[1], gzOutput);
 
 		System.err.println("Sort Complete");
 		return(0);
@@ -82,10 +84,10 @@ private String validateInput() throws IOException {
 		}
 		if(!"".equals(r)){ return(r); }
 		//check input extensions
-		if(!"gff".equals(ExtensionFileFilter.getExtension(gffFile))){
+		if(!"gff".equals(ExtensionFileFilter.getExtensionIgnoreGZ(gffFile))){
 			r += "(!)Is this a GFF file? Check extension: " + gffFile.getName() + "\n";
 		}
-		if(!"cdt".equals(ExtensionFileFilter.getExtension(cdtFile))){
+		if(!"cdt".equals(ExtensionFileFilter.getExtensionIgnoreGZ(cdtFile))){
 			r += "(!)Is this a CDT file? Check extension: " + cdtFile.getName() + "\n";
 		}
 		// validate CDT as file, with consistent row size, and save row_size value
@@ -98,7 +100,7 @@ private String validateInput() throws IOException {
 
 		//set default output filename
 		if(outputBasename==null){
-			outputBasename = ExtensionFileFilter.stripExtension(gffFile) + "_SORT";
+			outputBasename = ExtensionFileFilter.stripExtensionIgnoreGZ(gffFile) + "_SORT";
 		//check output filename is valid
 		}else{
 			//no extension check

src/main/java/scriptmanager/cli/Coordinate_Manipulation/ShiftCoordCLI.java

@@ -78,8 +78,7 @@ private String validateInput() throws IOException {
 		if(outputFilepath==null){
 			String SUFFIX = shift < 0 ? "_shift" + shift + "bp." : "_shift+" + shift + "bp.";
 			SUFFIX += isGFF ? "gff" : "bed";
-			SUFFIX += gzOutput ? ".gz" : "";
-			outputFilepath = ExtensionFileFilter.stripExtension(input) + SUFFIX;
+			outputFilepath = ExtensionFileFilter.stripExtensionIgnoreGZ(input) + SUFFIX;
 		//check output filename is valid
 		}else{
 			//no extension check

src/main/java/scriptmanager/cli/File_Utilities/ConvertBEDChrNamesCLI.java

@@ -42,6 +42,7 @@ public ConvertBEDChrNamesCLI(){}
 
 	@Option(names = {"-m", "--chrmt"}, description = "converter will map \"chrM\" --> \"chrmt\" (default with no flag is \"chrmt\" --> \"chrM\")")
 	private boolean useChrmt = false;
+
 	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
 	private boolean gzOutput = false;
 
@@ -88,13 +89,8 @@ private String validateInput() throws IOException {
 		if (output == null) {
 			// Set suffix format
 			String SUFFIX = toArabic ? "_toRoman.gff" : "_toArabic.gff";
-			SUFFIX += gzOutput ? ".gz" : "";
 			// Set output filepath with name and output directory
-			String OUTPUT = ExtensionFileFilter.stripExtension(coordFile);
-			// Strip second extension if input has ".gz" first extension
-			if (coordFile.getName().endsWith(".gff.gz")) {
-				OUTPUT = ExtensionFileFilter.stripExtensionPath(new File(OUTPUT)) ;
-			}
+			String OUTPUT = ExtensionFileFilter.stripExtensionIgnoreGZ(coordFile);
 			output = new File(OUTPUT + SUFFIX);
 		}else{
 			//check directory

src/main/java/scriptmanager/cli/File_Utilities/ConvertGFFChrNamesCLI.java

@@ -43,6 +43,7 @@ public ConvertGFFChrNamesCLI(){}
 
 	@Option(names = {"-m", "--chrmt"}, description = "converter will map \"chrM\" --> \"chrmt\" (default with no flag is \"chrmt\" --> \"chrM\")")
 	private boolean useChrmt = false;
+
 	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
 	private boolean gzOutput = false;
 
@@ -89,13 +90,8 @@ private String validateInput() throws IOException {
 		if (output == null) {
 			// Set suffix format
 			String SUFFIX = toArabic ? "_toRoman.bed" : "_toArabic.bed";
-			SUFFIX += gzOutput ? ".gz" : "";
 			// Set output filepath with name and output directory
-			String OUTPUT = ExtensionFileFilter.stripExtension(coordFile);
-			// Strip second extension if input has ".gz" first extension
-			if (coordFile.getName().endsWith(".bed.gz")) {
-				OUTPUT = ExtensionFileFilter.stripExtensionPath(new File(OUTPUT)) ;
-			}
+			String OUTPUT = ExtensionFileFilter.stripExtensionIgnoreGZ(coordFile);
 			output = new File(OUTPUT + SUFFIX);
 		}else{
 			//check directory

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

@@ -38,6 +38,8 @@ public BEDPeakAligntoRefCLI(){}
 
 	@Option(names = {"-o", "--output"}, description = "Specify output file (default = <peakBED>_<refBED>_Output.cdt)")
 	private File output = null;
+	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
+	private boolean gzOutput = false;
 
 	/**
 	 * Runs when this subcommand is called, running script in respective script package with user defined arguments
@@ -53,7 +55,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		BEDPeakAligntoRef script_obj = new BEDPeakAligntoRef(refBED, peakBED, output, null);
+		BEDPeakAligntoRef script_obj = new BEDPeakAligntoRef(refBED, peakBED, output, null, gzOutput);
 		script_obj.run();
 
 		System.err.println( "Peak Align Complete." );	

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

@@ -32,6 +32,8 @@ public class FilterBEDbyProximityCLI implements Callable<Integer> {
 
 	@Option(names = {"-o", "--output"}, description = "Specify basename for output files (default = <bedFilename>_<exclusionNum>bp)")
 	private String outputBasename = null;
+	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
+	private boolean gzOutput = false;
 	@Option(names = {"-e", "--exclusion"}, description = "exclusion distance in bp (default=100)")
 	private int exclusion = 100;
 
@@ -49,7 +51,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		FilterBEDbyProximity script_obj = new FilterBEDbyProximity(bedFile, exclusion, outputBasename, null);
+		FilterBEDbyProximity script_obj = new FilterBEDbyProximity(bedFile, exclusion, outputBasename, null, gzOutput);
 		script_obj.run();
 
 		System.err.println( "Filter Complete." );

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

@@ -32,6 +32,8 @@ 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 = "gzip output (default=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)")
@@ -53,7 +55,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		RandomCoordinate.execute(genomeName, numSites, window, formatIsBed, output); 
+		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

@@ -32,6 +32,8 @@ 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 = "gzip output (default=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)")
@@ -51,7 +53,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		TileGenome.execute(genomeName, window, formatIsBed, output);
+		TileGenome.execute(genomeName, window, formatIsBed, output, gzOutput);
 
 		System.err.println( "Genomic Tiling Complete." );
 		return(0);

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

@@ -40,6 +40,8 @@ public AggregateDataCLI() {}
 	private boolean fileList = false;
 	@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 = "gzip output (default=false)")
+	private boolean gzOutput = false;
 
 	@ArgGroup(exclusive = true, heading = "Aggregation Method%n")
 	AggType aggr = new AggType();
@@ -84,7 +86,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		AggregateData script_obj = new AggregateData(matFiles, output, merge, startROW, startCOL, aggType);
+		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

@@ -32,6 +32,8 @@ 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 = "gzip output (default=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 = "")
@@ -54,7 +56,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}		
 
-		ScaleMatrix script_obj = new ScaleMatrix(matrixFile, output, scale, startROW, startCOL);
+		ScaleMatrix script_obj = new ScaleMatrix(matrixFile, output, scale, startROW, startCOL, gzOutput);
 		script_obj.run();
 
 		System.err.println("All Matrices Scaled.");
@@ -72,7 +74,7 @@ private String validateInput() throws IOException {
 		//no check ext
 		//set default output filename
 		if(output==null){
-			output = new File(ExtensionFileFilter.stripExtension(matrixFile) + "_SCALE." + ExtensionFileFilter.getExtension(matrixFile)); 
+			output = new File(ExtensionFileFilter.stripExtensionIgnoreGZ(matrixFile) + "_SCALE." + ExtensionFileFilter.getExtensionIgnoreGZ(matrixFile)); 
 		//check output filename is valid
 		}else if( output.isDirectory() ){
 			r += "(!)Must indicate file (not a directory) for your output.";