remove in/out extension restrictions on CLI tools

This commit removes unnecessary extension filename validation from the CLI tools. This validation is too restrictive and interferes with development of Galaxy wrappers by forcing workarounds (Galaxy uses `.dat` extensions).

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

@@ -94,10 +94,6 @@ private String validateInput() throws IOException {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
@@ -116,12 +112,6 @@ private String validateInput() throws IOException {
 			if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }
 		//check output filename is valid
 		}else{
-			//check ext
-			try{
-				if(!"bed".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 + ".bed\n"; }
 			//check directory
 			if(output.getParent()==null){
 	// 			System.err.println("default to current directory");

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

@@ -94,10 +94,6 @@ private String validateInput() throws IOException {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
@@ -116,12 +112,6 @@ private String validateInput() throws IOException {
 			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 GFF extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".gff\n";
-				}
-			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use GFF extension for output filename. Try: " + output + ".gff\n"; }
 			//check directory
 			if(output.getParent()==null){
 	// 			System.err.println("default to current directory");

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

@@ -89,10 +89,6 @@ private String validateInput() throws IOException {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){

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

@@ -91,10 +91,6 @@ private String validateInput() throws IOException {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
@@ -113,12 +109,6 @@ private String validateInput() throws IOException {
 			if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }
 		//check output filename is valid
 		}else{
-			//check ext
-			try{
-				if(!"tab".equals(ExtensionFileFilter.getExtension(output))){
-					r += "(!)Use \".tab\" extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".tab\n";
-				}
-			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use \".tab\" extension for output filename. Try: " + output + ".tab\n"; }
 			//check directory
 			if(output.getParent()==null){
 	// 			System.err.println("default to current directory");

src/main/java/scriptmanager/cli/BAM_Manipulation/FilterforPIPseqCLI.java

@@ -73,14 +73,6 @@ private String validateInput() throws IOException {
 		if (!r.equals("")) {
 			return (r);
 		}
-		// check input extensions
-		ExtensionFileFilter faFilter = new ExtensionFileFilter("fa");
-		if (!faFilter.accept(genomeFASTA)) {
-			r += "(!)Is this a FASTA file? Check extension: " + genomeFASTA.getName() + "\n";
-		}
-		if (!"bam".equals(ExtensionFileFilter.getExtension(bamFile))) {
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		// check BAI exists
 		File f = new File(bamFile + ".bai");
 		if (!f.exists() || f.isDirectory()) {
@@ -98,16 +90,6 @@ private String validateInput() throws IOException {
 			output = new File(ExtensionFileFilter.stripExtension(bamFile) + "_PSfilter.bam");
 			// check output filename is valid
 		} else {
-			// check ext
-			try {
-				if (!"bam".equals(ExtensionFileFilter.getExtension(output))) {
-					r += "(!)Use BAM extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output)
-							+ ".bam\n";
-				}
-			} catch (NullPointerException e) {
-				r += "(!)Output filename must have extension: use BAM extension for output filename. Try: "
-						+ ExtensionFileFilter.stripExtension(output) + ".bam\n";
-			}
 			// check directory
 			if (output.getParent() == null) {
 // 					System.err.println("default to current directory");

src/main/java/scriptmanager/cli/BAM_Statistics/BAMGenomeCorrelationCLI.java

@@ -123,9 +123,6 @@ private String validateInput() throws IOException {
 			//check input exists
 			if(!BAM.exists()|| BAM.isDirectory()){
 				r += "(!)BAM[" + x + "] file does not exist: " + BAM.getName() + "\n";
-			//check input extensions
-			}else if(!"bam".equals(ExtensionFileFilter.getExtension(BAM))){
-				r += "(!)Is this a BAM file? Check extension: " + BAM.getName() + "\n";
 			//check BAI exists
 			}else if(!BAI.exists() || BAI.isDirectory()){
 				r += "(!)BAI Index File does not exist for: " + BAM.getName() + "\n";
@@ -137,7 +134,6 @@ private String validateInput() throws IOException {
 			outputBasename = new File("correlation_matrix");
 		//check output filename is valid
 		}else{
-			//no check ext
 			//check directory
 			if(outputBasename.getParent()==null){
 // 				System.err.println("default to current directory");

src/main/java/scriptmanager/cli/BAM_Statistics/PEStatsCLI.java

@@ -62,10 +62,6 @@ private String validateInput() throws IOException {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
@@ -77,7 +73,6 @@ private String validateInput() throws IOException {
 			outputBasename = new File(ExtensionFileFilter.stripExtension(bamFile));
 		//check output filename is valid
 		}else{
-			//no check ext
 			//check directory
 			if(outputBasename.getParent()==null){
 // 				System.err.println("default to current directory");

src/main/java/scriptmanager/cli/BAM_Statistics/SEStatsCLI.java

@@ -53,10 +53,6 @@ private String validateInput() throws IOException {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
@@ -68,7 +64,6 @@ private String validateInput() throws IOException {
 			output = new File(ExtensionFileFilter.stripExtension(bamFile) + "_stats.txt");
 		//check output filename is valid
 		}else{
-			//no check ext
 			//check directory
 			if(output.getParent()==null){
 // 				System.err.println("default to current directory");

src/main/java/scriptmanager/cli/Figure_Generation/MergeHeatMapCLI.java

@@ -30,8 +30,7 @@ public class MergeHeatMapCLI implements Callable<Integer> {
 	@Parameters(index = "1", description = "Second(anti) PNG heatmap to merge, input2")
 	private File antiFile;
 
-	@Option(names = { "-o",
-			"--output" }, description = "specify output filename, please use PNG extension\n(default=\"<senseFile>_merged.png\" appended to the name in working directory of ScriptManager")
+	@Option(names = { "-o", "--output" }, description = "specify output filename, please use PNG extension\n(default=\"<senseFile>_merged.png\" appended to the name in working directory of ScriptManager")
 	private File output = null;
 
 	@Override
@@ -64,29 +63,12 @@ private String validateInput() throws IOException {
 		if (!r.equals("")) {
 			return (r);
 		}
-		// check input extensions
-		if (!"png".equals(ExtensionFileFilter.getExtension(senseFile))) {
-			r += "(!)Is this a PNG file? Check extension: " + senseFile.getName() + "\n";
-		}
-		if (!"png".equals(ExtensionFileFilter.getExtension(antiFile))) {
-			r += "(!)Is this a PNG file? Check extension: " + antiFile.getName() + "\n";
-		}
 		// set default output filename
 		if (output == null) {
 			String NAME = ExtensionFileFilter.stripExtension(senseFile);
 			output = new File(NAME + "_merged.png");
 			// check output filename is valid
 		} else {
-			// check ext
-			try {
-				if (!"png".equals(ExtensionFileFilter.getExtension(output))) {
-					r += "(!)Use PNG extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output)
-							+ ".png\n";
-				}
-			} catch (NullPointerException e) {
-				r += "(!)Output filename must have extension: use PNG extension for output filename. Try: " + output
-						+ ".png\n";
-			}
 			// check directory
 			if (output.getParent() == null) {
 // 				System.err.println("default to current directory");

src/main/java/scriptmanager/cli/Figure_Generation/ThreeColorHeatMapCLI.java

@@ -164,26 +164,12 @@ private String validateInput() throws IOException {
 			r += "(!)CDT file does not exist: " + CDT.getName() + "\n";
 			return (r);
 		}
-		// check input extensions
-		if (!"cdt".equals(ExtensionFileFilter.getExtension(CDT))) {
-			r += "(!)Is this a CDT file? Check extension: " + CDT.getName() + "\n";
-		}
 		// set default output filename
 		if (output == null) {
 			String NAME = ExtensionFileFilter.stripExtension(CDT);
 			output = new File(NAME + "_" + scaleType + ".png");
 			// check output filename is valid
 		} else {
-			// check ext
-			try {
-				if (!"png".equals(ExtensionFileFilter.getExtension(output))) {
-					r += "(!)Use PNG extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output)
-							+ ".png\n";
-				}
-			} catch (NullPointerException e) {
-				r += "(!)Output filename must have extension: use PNG extension for output filename. Try: " + output
-						+ ".png\n";
-			}
 			// check directory
 			if (output.getParent() == null) {
 // 				System.err.println("default to current directory");

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

@@ -60,24 +60,11 @@ private String validateInput() throws IOException {
 			r += "(!)BED-ref file does not exist: " + refBED.getName() + "\n";
 		}
 		if(!r.equals("")){ return(r); }
-		//check input extensions
-		if(!"bed".equals(ExtensionFileFilter.getExtension(peakBED))){
-			r += "(!)Is this a BED file? Check extension: " + peakBED.getName() + "\n";
-		}
-		if(!"bed".equals(ExtensionFileFilter.getExtension(refBED))){
-			r += "(!)Is this a BED file? Check extension: " + refBED.getName() + "\n";
-		}
 		//set default output filename
 		if(output==null){
 			output = new File(ExtensionFileFilter.stripExtension(peakBED) + "_" + ExtensionFileFilter.stripExtension(refBED) + "_Output.cdt");
 		//check output filename is valid
 		}else{
-			//check ext
-			try{
-				if(!"cdt".equals(ExtensionFileFilter.getExtension(output))){
-					r += "(!)Use CDT extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".cdt\n";
-				}
-			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use CDT extension for output filename. Try: " + output + ".cdt\n"; }
 			//check directory
 			if(output.getParent()==null){
 // 				System.err.println("default to current directory");

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

@@ -57,16 +57,11 @@ private String validateInput() throws IOException {
 			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(outputBasename==null){
 			outputBasename = ExtensionFileFilter.stripExtension(bedFile) + "_" + Integer.toString(exclusion) + "bp";
 		//check output filename is valid
 		}else{
-			//no check ext
 			//check directory
 			File tmpOut = new File(outputBasename);
 			if(tmpOut.getParent()==null){

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

@@ -62,12 +62,6 @@ private String validateInput() throws IOException {
 			output = new File("random_coordinates_" + genomeName + "_" + numSites + "sites_" + window + "bp." + ext);
 		//check output filename is valid
 		}else{
-			//check ext
-			try{
-				if(!ext.equals(ExtensionFileFilter.getExtension(output))){
-					r += "(!)Use \"." + ext.toUpperCase() + "\" extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + "." + ext + "\n";
-				}
-			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use \"." + ext.toUpperCase() + "\" extension for output filename. Try: " + output + "." + ext + "\n"; }
 			//check directory
 			if(output.getParent()==null){
 	// 			System.err.println("default to current directory");

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

@@ -60,12 +60,6 @@ private String validateInput() throws IOException {
 			output = new File(genomeName + "_" + window + "bp." + ext);
 		//check output filename is valid
 		}else{
-			//check ext
-			try{
-				if(!ext.equals(ExtensionFileFilter.getExtension(output))){
-					r += "(!)Use \"." + ext.toUpperCase() + "\" extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + "." + ext + "\n";
-				}
-			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use \"." + ext.toUpperCase() + "\" extension for output filename. Try: " + output + "." + ext + "\n"; }
 			//check directory
 			if(output.getParent()==null){
 	// 			System.err.println("default to current directory");

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

@@ -86,19 +86,11 @@ private String validateInput() throws IOException {
 			if(!controlBAM.exists()){ r += "(!)BAM(control) file does not exist: " + controlBAM.getName() + "\n"; }
 		}
 		if(!r.equals("")){ return(r); }
-		//check input extensions & BAI exists
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM(input) file? Check extension: " + bamFile.getName() + "\n";
-		}
+		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
 			r += "(!)BAI Index File does not exist for: " + bamFile.getName() + "\n";
 		}
-		if(blacklistFilter!=null){
-			if(!"bed".equals(ExtensionFileFilter.getExtension(blacklistFilter))){
-				r += "(!)Is this a BED file? Check extension: " + blacklistFilter.getName() + "\n";
-			}
-		}
 		if(controlBAM!=null){
 			if(!"bam".equals(ExtensionFileFilter.getExtension(controlBAM))){
 				r += "(!)Is this a BAM(control) file? Check extension: " + controlBAM.getName() + "\n";
@@ -114,7 +106,6 @@ private String validateInput() throws IOException {
 		//check output filename is valid
 		}else{
 			File tempOut = new File(outputBasename);
-			//no check ext
 			//check directory
 			if(tempOut.getParent()==null){
 // 				System.err.println("default to current directory");

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

@@ -187,7 +187,6 @@ private String validateInput() throws IOException {
 		//check output COMPOSITE filename is valid
 		if(outputOptions.outputComposite!="composite_average.out"){
 			File output = new File(outputOptions.outputComposite);
-			//no check ext
 			//check directory
 			if(output.getParent()==null){
 // 				System.err.println("default to current directory");

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

@@ -124,14 +124,6 @@ private String validateInput() throws IOException {
 		if (!r.equals("")) {
 			return (r);
 		}
-		// check input extensions
-		ExtensionFileFilter faFilter = new ExtensionFileFilter("fa");
-		if (!faFilter.accept(genomeFASTA)) {
-			r += "(!)Is this a FASTA file? Check extension: " + genomeFASTA.getName() + "\n";
-		}
-		if (!"bed".equals(ExtensionFileFilter.getExtension(bedFile))) {
-			r += "(!)Is this a BED file? Check extension: " + bedFile.getName() + "\n";
-		}
 		// set default output filename
 		if (outputBasename == null) {
 			outputBasename = ExtensionFileFilter.stripExtension(bedFile);

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

@@ -114,18 +114,12 @@ private String validateInput() throws IOException {
 			r += "(!)FASTA file does not exist: " + fastaFile.getName() + "\n";
 			return (r);
 		}
-		// check input extensions
-		ExtensionFileFilter faFilter = new ExtensionFileFilter("fa");
-		if (!faFilter.accept(fastaFile)) {
-			r += "(!)Is this a FASTA file? Check extension: " + fastaFile.getName() + "\n";
-		}
 		// set default output filename
 		if (outputBasename == null) {
 			outputBasename = ExtensionFileFilter.stripExtension(fastaFile);
 			// check output filename is valid
 		} else {
 			String outParent = new File(outputBasename).getParent();
-			// no extension check
 			// check directory
 			if (outParent == null) {
 // 				System.err.println("default to current directory");