Merge branch 'master' into dev

Author: owlang

src/cli/Figure_Generation/ThreeColorHeatMapCLI.java

@@ -76,7 +76,7 @@ static class MaxGroup {
 	@Option(names = {"-0", "--include-zeros"}, description = "used with `-p` flag, indicating exclusion of zero values when calculating percentile thresholds")
 	private boolean includeZeros = false;
 
-	@ArgGroup(multiplicity = "0..1", heading = "%nSelect heatmap colors:%n")
+	@ArgGroup(multiplicity = "0..1", exclusive=false, heading = "%nSelect heatmap colors:%n")
 	private ColorGroup color = new ColorGroup();
 	static class ColorGroup {
 		@Option(names = {"-cn", "--color-min"}, description = "Color indicating minimum values (default=YELLOW) For custom color: type hexadecimal string to represent colors (e.g. \"FF0000\" is hexadecimal for red).\n See <http://www.javascripter.net/faq/rgbtohex.htm> for some color options with their corresponding hex strings.\n")
@@ -88,7 +88,20 @@ static class ColorGroup {
 		@Option(names = {"-ca", "--color-nan"}, description = "Color indicating not-a-number values (default=GRAY) For custom color: type hexadecimal string to represent colors (e.g. \"FF0000\" is hexadecimal for red).\n See <http://www.javascripter.net/faq/rgbtohex.htm> for some color options with their corresponding hex strings.\n")
 		private String nan = null;
 	}
-
+	
+	@ArgGroup(multiplicity = "0..1", exclusive=false, heading = "%nSelect transparency of heatmap colors (alpha channel):%n")
+	private AlphaGroup alpha = new AlphaGroup();
+	static class AlphaGroup {
+		@Option(names = {"-tn", "--transparent-min"}, description = "Value indicating transparency of minimum values, 0 to 255 (default=255)\n")
+		private int min = 255;
+		@Option(names = {"-td", "--transparent-mid"}, description = "Value indicating transparency of middle values, 0 to 255  (default=255)\n")
+		private int mid = 255;
+		@Option(names = {"-tx", "--transparent-max"}, description = "Value indicating transparency of maximum values, 0 to 255  (default=255)\n")
+		private int max = 255;
+		@Option(names = {"-ta", "--transparent-nan"}, description = "Value indicating transparency of not-a-number values, 0 to 255  (default=255)\n")
+		private int nan = 255;
+	}
+	
 	String scaleType = "treeview";
 	//Colors from JavaTreeview microarray software
 	Color CMAX = new Color(254,255,0,255);
@@ -217,6 +230,16 @@ private String validateInput() throws IOException {
 			System.err.println("Decoding NaN color: 0x" + color.nan);
 			CNAN = Color.decode("0x" + color.nan);
 		}
+		// check that Alpha channel/transparency values are formatted properly and decode/assign colors
+		if (alpha.max<0 || alpha.max>255) { r += "(!)Alpha/transparency value for higher values (max) must be a numeric 0 to 255\n"; }
+		else { CMAX = new Color(CMAX.getRed(), CMAX.getGreen(), CMAX.getBlue(), alpha.max); }
+		if (alpha.mid<0 || alpha.mid>255) { r += "(!)Alpha/transparency value for middling values (mid) must be a numeric 0 to 255\n"; }
+		else { CMID = new Color(CMID.getRed(), CMID.getGreen(), CMID.getBlue(), alpha.mid); }
+		if (alpha.min<0 || alpha.min>255) { r += "(!)Alpha/transparency value for lower values(min) must be a numeric 0 to 255\n"; }
+		else { CMIN = new Color(CMIN.getRed(), CMIN.getGreen(), CMIN.getBlue(), alpha.min); }
+		if (alpha.nan<0 || alpha.nan>255) { r += "(!)Alpha/transparency value for invalid/non-numeric values(NaN) must be a numeric 0 to 255\n"; }
+		else { CNAN = new Color(CNAN.getRed(), CNAN.getGreen(), CNAN.getBlue(), alpha.nan); }
+		
 		// assign vals for contrast thresholds and set bools
 		if(maxGroup.percentile!=null) {
 			MAX = maxGroup.percentile;

src/cli/Figure_Generation/TwoColorHeatMapCLI.java

@@ -56,7 +56,6 @@ public class TwoColorHeatMapCLI implements Callable<Integer> {
 
 	@ArgGroup(exclusive = true, multiplicity = "0..1", heading = "%nSelect heatmap color:%n\t@|fg(red) (select no more than one of these options)|@%n")
 	private ColorGroup color = new ColorGroup();
-
 	static class ColorGroup {
 		@Option(names = { "--black" }, description = "Use the color black for generating the heatmap (default)")
 		private boolean black = false;
@@ -68,6 +67,12 @@ static class ColorGroup {
 				"--color" }, description = "For custom color: type hexadecimal string to represent colors (e.g. \"FF0000\" is hexadecimal for red).\n See <http://www.javascripter.net/faq/rgbtohex.htm> for some color options with their corresponding hex strings.\n")
 		private String custom = null;
 	}
+	@Option(names = { "-t", "--transparent" }, description = "Value indicating transparency of heatmap, 0 to 255  (default=255)\n")
+	private int alpha = 255;
+
+	@Option(names = { "-b", "--background" }, description = "Set a transparent background for the heatmap minimum values (default=white)\n")
+	private boolean transparentBackground = false;
+	
 
 	String scaleType = "treeview";
 	Color MAXCOLOR = Color.BLACK;
@@ -84,7 +89,7 @@ public Integer call() throws Exception {
 
 		// Generate HeatMap
 		TwoColorHeatMap script_object = new TwoColorHeatMap(CDT, MAXCOLOR, startROW, startCOL, pixelHeight, pixelWidth,
-				scaleType, absolute, percentile, output, true);
+				scaleType, absolute, percentile, output, true, transparentBackground);
 		script_object.run();
 
 		System.err.println("Image Generated.");
@@ -114,16 +119,6 @@ private String validateInput() throws IOException {
 			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");
@@ -136,14 +131,7 @@ private String validateInput() throws IOException {
 		if (compression < 1 || compression > 4) {
 			r += "(!)Compression must be integer 1-4. Please select from the available compression types.";
 		}
-		// check that hex string is formatted properly
-		if (color.custom != null) {
-			Pattern hexColorPat = Pattern.compile("[0-9A-Fa-f]{6}");
-			Matcher m = hexColorPat.matcher(color.custom);
-			if (!m.matches()) {
-				r += "(!)Color must be formatted as a hexidecimal String!\n\tExpected input string format: \"[0-9A-Fa-f]{6}\"";
-			}
-		}
+
 		// check scaling is valid input
 		if (absolute == -999 && percentile == -999) {
 			absolute = 10;
@@ -165,8 +153,16 @@ private String validateInput() throws IOException {
 			MAXCOLOR = Color.BLUE;
 		} else if (color.custom != null) {
 			System.err.println("Decoding color: 0x" + color.custom);
-			MAXCOLOR = Color.decode("0x" + color.custom);
+			// check that hex string is formatted properly
+			Pattern hexColorPat = Pattern.compile("[0-9A-Fa-f]{6}");
+			Matcher m = hexColorPat.matcher(color.custom);
+			if (!m.matches()) {
+				r += "(!)Color must be formatted as a hexidecimal String!\n\tExpected input string format: \"[0-9A-Fa-f]{6}\"";
+			} else { MAXCOLOR = Color.decode("0x" + color.custom); }
 		}
+		// check that Alpha channel/transparency values are formatted properly and decode/assign colors
+		if (alpha<0 || alpha>255) { r += "(!)Alpha/transparency value for higher values (max) must be a numeric 0 to 255\n"; }
+		else { MAXCOLOR = new Color(MAXCOLOR.getRed(), MAXCOLOR.getGreen(), MAXCOLOR.getBlue(), alpha); }
 
 		return (r);
 	}

src/cli/Read_Analysis/TagPileupCLI.java

@@ -58,6 +58,18 @@ static class OutputOptions{
 		private boolean tab = false;
 	}
 
+	//Aspect
+	@ArgGroup(exclusive = true, multiplicity = "0..1", heading = "%nSelect Aspect of Read to output:%n\t@|fg(red) (select no more than one of these options)|@%n")
+	AspectType aspectType = new AspectType();
+	static class AspectType {
+		@Option(names = {"-5", "--five-prime"}, description = "pileup of 5' end of read(default)")
+		boolean fiveprime = false;
+		@Option(names = {"-3", "--three-prime"}, description = "pileup of 3' end of read")
+		boolean threeprime = false;
+		@Option(names = {"-m", "--midpoint"}, description = "pileup fragment midpoints (require PE, combined)")
+		boolean midpoint = 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();
@@ -68,9 +80,6 @@ static class ReadType {
 		boolean read2 = false;
 		@Option(names = {"-a", "--all-reads"}, description = "pileup all reads")
 		boolean allreads = false;
-		@Option(names = {"-m", "--midpoint"}, description = "pile midpoint (require PE and combined, -p --combined)")
-		boolean midpoint = false;
-		int finalRead = 0;
 	}
 
 	//Strand
@@ -148,15 +157,15 @@ public Integer call() throws Exception {
 	private String validateInput() throws IOException {
 		String r = "";
 
-		//check ReadType, interpret booleans for int value
-		if(readType.read1){ readType.finalRead = 0; }
-		else if(readType.read2){ readType.finalRead = 1; }
-		else if(readType.allreads){ readType.finalRead = 2; }
-		else if(readType.midpoint){
-			readType.finalRead = 3;
-			filterOptions.requirePE = true;
-			combStatus = true;
-		}
+		// Set ASPECT
+		if(aspectType.fiveprime) { p.setAspect(0); }
+		else if(aspectType.threeprime) { p.setAspect(1); }
+		else if(aspectType.midpoint) { p.setAspect(2); }
+
+		// Set READ
+		if(readType.read1){ p.setRead(0); }
+		else if(readType.read2){ p.setRead(1); }
+		else if(readType.allreads){ p.setRead(2); }
 
 		//check input extensions
 		if(!"bed".equals(ExtensionFileFilter.getExtension(bedFile))){
@@ -192,39 +201,15 @@ else if(readType.midpoint){
 			}
 		}
 
-		//set default output MATRIX (if output MATRIX not to be output)
-		if(outputOptions.outputMatrix.size()>1){
-			outputOptions.outputMatrix.set(0,null);
-		//set default output MATRIX basename (allow scripts/*/TagPileup to generate ret of filename)
-		} else if(outputOptions.outputMatrix.size()==0){  //generate default basename
-			String readString = "read1";
-			if(readType.finalRead == 1) { readString = "read2"; }
-			else if(readType.finalRead == 2) { readString = "allreads"; }
-			else if(readType.finalRead == 3) { readString = "midpoint"; }
-			outputOptions.outputMatrix.add( 
-				ExtensionFileFilter.stripExtension(new File(bedFile.getName())) + "_" +
-				ExtensionFileFilter.stripExtension(new File(bamFile.getName())) + "_" + readString);
-		//check output filename is valid
-		}else{										//check basename
-			File output = new File(outputOptions.outputMatrix.get(0));
-			//no extension check b/c basename should have no extension
-			//check directory
-			if(output.getParent()==null){
-// 				System.err.println("default to current directory");
-			} else if(!new File(output.getParent()).exists()){
-				r += "(!)Check output.MATRIX directory exists: " + output.getParent() + "\n";
-			}
-		}
-		
 		//validate smooth params
 		if(smoothType.winVals!=-9999 && smoothType.winVals<1){ r += "(!)Invalid Smoothing Window Size. Must be larger than 0 bins, winSize=" + smoothType.winVals + "\n"; }
 		if(smoothType.winVals!=-9999 && smoothType.winVals%2==0){ r += "(!)Invalid Smoothing Window Size. Must be odd for symmetrical smoothing (so that the window is centered properly), winSize=" + smoothType.winVals + "\n"; }
 		if(smoothType.gaussVals[0]!=-9999 && smoothType.gaussVals[0]<1){ r += "(!)Invalid Standard Deviation Size. Must be larger than 0 bins, stdSize=" + smoothType.gaussVals[0] + "\n"; }
 		if(smoothType.gaussVals[1]!=-9999 && smoothType.gaussVals[1]<1){ r += "(!)Invalid Number of Standard Deviations. Must be larger than 0 standard deviations, stdNum=" + smoothType.gaussVals[1] + "\n"; }
 
 		//set require PE for appropriate flags
-		if( filterOptions.MIN_INSERT!=-9999 || filterOptions.MAX_INSERT!=-9999){ filterOptions.requirePE = true; }
-		if( readType.midpoint ){ filterOptions.requirePE = true; }
+		p.setPErequire(filterOptions.requirePE);
+		if( filterOptions.MIN_INSERT!=-9999 || filterOptions.MAX_INSERT!=-9999 || p.getAspect()==2) { p.setPErequire(true); }
 
 		//validate shift, binSize, and CPUs
 		if(calcOptions.shift<0){  r += "(!)Invalid shift! Must be non-negative, shift=" + calcOptions.shift + "\n"; }
@@ -238,38 +223,41 @@ else if(readType.midpoint){
 			r += "(!)MAX_INSERT must be larger/equal to MIN_INSERT: " + filterOptions.MIN_INSERT + "," + filterOptions.MAX_INSERT + "\n";
 		}
 
-		// LOAD UP PileupParameters OBJECT!
-				
-		//Set OUTPUT
-		if(outputOptions.outputMatrix.size()<=1){
-			p.setOutputType(2);														//default behavior
-			//check output type
-			if(outputOptions.cdt && outputOptions.tab) {							//both set? write error
-				r += "(!)Cannot flag both --cdt and --tab. Please choose one.";
-			} else if(outputOptions.tab){											//set tab
-				p.setOutputType(1);
-			}
-		}else{
-			outputOptions.outputMatrix.set(0,null);
-			p.setOutputType(0);   //no matrix output
-			if(outputOptions.cdt){
-				p.setOutputType(2);
-				outputOptions.outputMatrix.set(0,null);
-			} else if(outputOptions.tab) {
-				p.setOutputType(1);
-				outputOptions.outputMatrix.set(0,null);
+		// No Matrix Output
+		if(outputOptions.outputMatrix.size() > 1){
+			p.setOutputType(0);
+			if(outputOptions.cdt || outputOptions.tab) { r += "(!)Cannot flag --cdt or --tab without -M."; }
+		// Output Matrix
+		} else {
+			// Determine output type
+			p.setOutputType(2);
+			if(outputOptions.cdt && outputOptions.tab) { r += "(!)Cannot flag both --cdt and --tab. Please choose one."; }
+			else if(outputOptions.tab) { p.setOutputType(1); }
+			// No matrix basename specified
+			if(outputOptions.outputMatrix.size() == 0) {
+				outputOptions.outputMatrix.add(null);
+				if(p.getOutputDirectory() == null) {
+					p.setOutputDirectory(new File(System.getProperty("user.dir")));
+				}
+			// Validate matrix specified basename
+			} else if(outputOptions.outputMatrix.size() == 1) {
+				File output = new File(outputOptions.outputMatrix.get(0));
+				// Check parent directory is non-null and exists
+				if(output.getParent()!=null){
+					if(!new File(output.getParent()).exists()) {
+						r += "(!)Check output.MATRIX directory exists: " + output.getParent() + "\n";
+					}
+				}
 			}
 		}
-		p.setOutputCompositeStatus(true);
 
 		//Set COMPOSITE file
+		p.setOutputCompositeStatus(true);
 		p.setCompositePrintStream(new PrintStream(outputOptions.outputComposite));
 
-		//Set READ
-		p.setRead(readType.finalRead);
 		//Set STRAND
 		p.setStrand(0);
-		if(combStatus) { p.setStrand(1); }
+		if(combStatus || p.getAspect() == 2) { p.setStrand(1); }
 
 		//Set smooth type and parameters
 		if(smoothType.noSmooth){			//default behavior
@@ -299,9 +287,6 @@ else if(readType.midpoint){
 		p.setBlacklist(filterOptions.blacklistFilter);
 		p.setStandard(calcOptions.tagsEqual);
 
-		//Set PE requirement
-		p.setPErequire(filterOptions.requirePE);
-		
 		//Set output statuses
 		p.setGZIPstatus(outputOptions.zip);