Tagpileup overhaul

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))){
@@ -192,38 +201,14 @@ 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.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"; }
@@ -237,38 +222,41 @@ 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
@@ -298,9 +286,6 @@ 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);
 

src/objects/PileupParameters.java

@@ -3,31 +3,46 @@
 import java.io.File;
 import java.io.PrintStream;
 
+/**
+ * Object for storing pileup-related parameter information and constants.
+ * @see scripts.Read_Analysis.PileupScripts.PileupExtract
+ * @author William KM Lai
+ */
+
 public class PileupParameters {
-	//Directory to save matrix and composite into
-	private File OUTPUT = null;
-	//Composite values file if output
-	private PrintStream COMPOSITE = null;
+	//Read aspect
+	final static int FIVE = 0;
+	final static int THREE = 1;
+	final static int MIDPOINT = 2;
+	final static int FRAGMENT = 3;
+	private int ASPECT = PileupParameters.FIVE;
 
-	//Read type:
-	//  0=read1, 1=read2, 2=allreads, 3=midpoint
-	private int READ = 0;
+	//Read type
+	final static int READ1 = 0;
+	final static int READ2 = 1;
+	final static int ALLREADS = 2;
+	private int READ = PileupParameters.READ1;
 
-	//Strand type:
-	//  0=separate, 1=combined
-	private int STRAND = 0;
+	//Strand type
+	final static int COMBINED = 1;
+	final static int SEPARATE = 0;
+	private int STRAND = PileupParameters.SEPARATE;
+
+	//Transformation/smoothing type
+	final static int NO_SMOOTH = 0;
+	final static int WINDOW = 1;
+	final static int GAUSSIAN = 2;
+	private int TRANS = PileupParameters.NO_SMOOTH;
 
-	//Transformation/smoothing type:
-	//  0=no_smooth, 1=window, 2=gaussian
-	private int TRANS = 0;
 	//TRANS=1 parameters:  window size (#bins)
 	private int SMOOTH = 0;
-	//TRANS=2 parameters:  stdev window size (#bins) and number of standard devations
+	//TRANS=2 parameters:  stdev window size (#bins) and number of standard deviations
 	private int STDSIZE = 0;
-	private int STDNUM = 0;	
+	private int STDNUM = 0;
 
 	private int SHIFT = 0;
 	private int BIN = 1;
+	private int TAGEXTEND = 0;
 	private int CPU = 1;
 	private int OUTTYPE = 0;			//0=no output, 1=TAB, 2=CDT
 	private File BLACKLIST = null;
@@ -39,16 +54,23 @@ public class PileupParameters {
 
 	private int MIN_INSERT = -9999;
 	private int MAX_INSERT = -9999;
-
+
+	//Directory to save matrix and composite into
+	private File OUTPUT = null;
+	//Composite values file if output
+	private PrintStream COMPOSITE = null;
+
 	public void printAll(){
 		System.out.println( "<><><><><><><><><><><><><><><><><><><><>" );
 		System.out.println( "private File OUTPUT = " + OUTPUT );
 		System.out.println( "private String COMPOSITE = " + COMPOSITE );
 		System.out.println( "private int READ = " + READ );
+		System.out.println( "private int ASPECT = " + ASPECT );
 		System.out.println( "private int STRAND = " + STRAND );
 		System.out.println( "private int TRANS = " + TRANS );
 		System.out.println( "private int SHIFT = " + SHIFT );
 		System.out.println( "private int BIN = " + BIN );
+		System.out.println( "private int TAGEXTEND = " + TAGEXTEND );
 		System.out.println( "private int SMOOTH = " + SMOOTH );
 		System.out.println( "private int STDSIZE = " + STDSIZE );
 		System.out.println( "private int STDNUM = " + STDNUM );
@@ -144,6 +166,13 @@ public void setOutputDirectory(File oUTPUT) {
 		OUTPUT = oUTPUT;
 	}
 
+	public int getAspect() {
+		return ASPECT;
+	}
+	public void setAspect(int aSPECT) {
+		ASPECT = aSPECT;
+	}
+
 	public int getRead() {
 		return READ;
 	}
@@ -179,6 +208,13 @@ public void setBin(int bIN) {
 		BIN = bIN;
 	}
 
+	public int getTagExtend() {
+		return TAGEXTEND;
+	}
+	public void setTagExtend(int tAGEXTEND) {
+		TAGEXTEND = tAGEXTEND;
+	}
+
 	public int getSmooth() {
 		return SMOOTH;
 	}