implement read aspect with 3' ends

Relating to issue #70, this commit separates out the "Read Output" selection into the Read Output:{read1, read2, allreads} and the Read Aspect:{5prime, 3prime, midpoint}. This new feature has been checked on some simple test data for 3' end. This sets the new parameter structure for filling in with new features.

PileupParameters
-`ASPECT` variable added with descriptive comment and getter/setter methods
-`READ` variable's descriptive comments updated to remove "midpoint"
-`printall()` method updated to include `ASPECT` variable

PileupExtract
-Midpoint parameter check changed from `param.getRead() == 3` to `param.getAspect() == 2`
-Setting `mark` value now accounts for Read Aspect selected:
  -select start/left mark or end/right mark as appropriate for Read Aspect and reference strand values
  -Two places in the code: paired-end data conditional block and single-end conditional block
-some heavier boolean logic was added to the paired data `firstOfPairFlag()` check against the Read Output parameter so that it includes the Read Aspect parameter
-Separate SHIFT code into its own conditional block independently based on reference strand value alone

TagPileup
-update default file naming to include read aspect information

TagPileupWindow
-Window design:
  -add "Read Aspect" radiobutton selection options (with 5prime and 3prime and midpoint options)
  -remove "Midpoint" option from "Read Output"
  -components on right side of the window were vertically squished to fit with the new "Read Aspect" components (many `putConstraint()` lines changed)
-update assignment of Read Aspect & Read type values to the PileupParameters object in the `Task` class
-update radiobutton listeners to listen to "Read Aspect" choices rather than "Read Output" choices
-`allowReadChoice()` method was updated to enable/disable Read Type selection components (keep enable/disable strand components, separate/combined)

TagPileupCLI
-Add new argument group for assigning Read Aspect value
-Remove "midpoint" argument option from Read Type value
-propagate changes to affected midpoint validation lines

Author: owlang

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
@@ -148,11 +157,15 @@ public Integer call() throws Exception {
 	private String validateInput() throws IOException {
 		String r = "";
 
+		// 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); }
-		else if(readType.midpoint){ p.setRead(3); }
 
 		//check input extensions
 		if(!"bed".equals(ExtensionFileFilter.getExtension(bedFile))){
@@ -195,7 +208,7 @@ private String validateInput() throws IOException {
 
 		//set require PE for appropriate flags
 		p.setPErequire(filterOptions.requirePE);
-		if( filterOptions.MIN_INSERT!=-9999 || filterOptions.MAX_INSERT!=-9999 || p.getRead() == 3) { p.setPErequire(true); }
+		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"; }
@@ -243,7 +256,7 @@ private String validateInput() throws IOException {
 
 		//Set STRAND
 		p.setStrand(0);
-		if(combStatus || p.getRead() == 3) { p.setStrand(1); }
+		if(combStatus || p.getAspect() == 2) { p.setStrand(1); }
 
 		//Set smooth type and parameters
 		if(smoothType.noSmooth){			//default behavior

src/objects/PileupParameters.java

@@ -9,8 +9,11 @@ public class PileupParameters {
 	//Composite values file if output
 	private PrintStream COMPOSITE = null;
 
+	//Read aspect:
+	//  0=5prime end, 1=3prime end, 2=midpoint
+	private int ASPECT = 0;
 	//Read type:
-	//  0=read1, 1=read2, 2=allreads, 3=midpoint
+	//  0=read1, 1=read2, 2=allreads
 	private int READ = 0;
 
 	//Strand type:
@@ -45,6 +48,7 @@ public void printAll(){
 		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 );
@@ -144,6 +148,13 @@ public void setOutputDirectory(File oUTPUT) {
 		OUTPUT = oUTPUT;
 	}
 
+	public int getAspect() {
+		return ASPECT;
+	}
+	public void setAspect(int aSPECT) {
+		ASPECT = aSPECT;
+	}
+
 	public int getRead() {
 		return READ;
 	}

src/scripts/Read_Analysis/PileupScripts/PileupExtract.java

@@ -44,7 +44,7 @@ public void extract(BEDCoord coord) {
 		// Ugly hack to account for the fact that read 1 5' end may be outside the window of interest even though read 2 and the midpoint may be in range
 		// TODO FIX this into something more logical, probably check for read2 in region independently?
 		int MIDPOINT_ADJUST = 0;
-		if(param.getRead() == 3) { MIDPOINT_ADJUST = 300; }
+		if(param.getAspect() == 2) { MIDPOINT_ADJUST = 300; }
 
 		int BEDSTART = (int)coord.getStart();
 		int BEDSTOP = (int)coord.getStop();
@@ -63,26 +63,25 @@ else if(param.getTrans() == 2) {
 		TAG_S1 = new double[WINDOW];
 		if(STRAND == 0) TAG_S2 = new double[WINDOW];
 
-		//SAMRecords are 1-based
+		//SAMRecords are 1-based and inclusive
 		CloseableIterator<SAMRecord> iter = inputSam.query(coord.getChrom(), BEDSTART - QUERYWINDOW - SHIFT - MIDPOINT_ADJUST - 1, BEDSTOP + QUERYWINDOW + SHIFT + MIDPOINT_ADJUST + 1, false);
 		while (iter.hasNext()) {
 			//Create the record object 
-		    //SAMRecord is 1-based
 			SAMRecord sr = iter.next();
 
 			if(sr.getReadPairedFlag()) { //Must be PAIRED-END mapped
 				if((sr.getProperPairFlag() && param.getPErequire()) || !param.getPErequire()) { //Must either be properly paired if paired-end or don't care about requirement
-					//Read 1 and want Read 1, Read 2 and want Read 2, want any read, Read 1 and want midpoint
-					if((sr.getFirstOfPairFlag() && param.getRead() == 0) || (!sr.getFirstOfPairFlag() && param.getRead() == 1) || param.getRead() == 2 || (sr.getFirstOfPairFlag() && param.getRead() == 3)) {
+					// (Aspect=5/3prime and (Read 1 and want Read 1, Read 2 and want Read 2, want any read)) or Read 1 and want midpoint
+					if(((param.getAspect() == 0 || param.getAspect() == 1) && ((sr.getFirstOfPairFlag() && param.getRead() == 0) || (!sr.getFirstOfPairFlag() && param.getRead() == 1) || param.getRead() == 2 )) || (sr.getFirstOfPairFlag() && param.getAspect() == 2)) {
+						// Set marker (left side default, right side if positive strand and 5 prime or negative strand and 3 prime
 						int mark = sr.getUnclippedStart() - 1;
-						if(sr.getReadNegativeStrandFlag()) { 
+						if((param.getAspect() == 0 && sr.getReadNegativeStrandFlag()) || (param.getAspect() == 1 && !sr.getReadNegativeStrandFlag())) {
 							mark = sr.getUnclippedEnd() - 1;
-							mark -= SHIFT; //SHIFT DATA HERE IF NECCESSARY
-						} else { mark += SHIFT; }
+						}
 
 						if(sr.getProperPairFlag()) { //prevent cases where non-properly paired Read1 gets to this point
-							//Find midpoint if read flag == 3
-							if(param.getRead() == 3) {
+							//Find midpoint if aspect flag == 2
+							if(param.getAspect() == 2) {
 								if(sr.getInferredInsertSize()>0) {
 									mark = sr.getAlignmentStart() - 1 + (sr.getInferredInsertSize() / 2);
 								} else if(sr.getInferredInsertSize()<0) {
@@ -98,12 +97,16 @@ else if(param.getTrans() == 2) {
 							// Apply insert size filters
 							if(Math.abs(sr.getInferredInsertSize()) < param.getMinInsert() && param.getMinInsert() != -9999) { continue; } //Test for MIN insert size cutoff here
 							if(Math.abs(sr.getInferredInsertSize()) > param.getMaxInsert() && param.getMaxInsert() != -9999) { continue; } //Test for MAX insert size cutoff here
-						} else if(param.getRead() == 3) { continue; } // Make sure that midpoint pileup must come from properly paired read
+						} else if(param.getAspect() == 2) { continue; }		// Make sure that midpoint pileup must come from properly paired read
 
+						// Shift as needed
+						if(sr.getReadNegativeStrandFlag()) { mark -= SHIFT; }
+						else { mark += SHIFT; }
+
 						//Adjust tag start to be within array reference
 						mark -= (BEDSTART - QUERYWINDOW);
 
-	                    //Increment Final Array keeping track of pileup
+						//Increment Final Array keeping track of pileup
 						if(mark >= 0 && mark < TAG_S1.length) {
 							if(STRAND == 0) {
 								if(!sr.getReadNegativeStrandFlag() && coord.getDir().equals("-")) { TAG_S2[mark] += 1; }
@@ -116,12 +119,17 @@ else if(param.getTrans() == 2) {
 						}
 					}
 				}
-			} else if(param.getRead() == 0 || param.getRead() == 2) { //Also outputs if not paired-end since by default it is read-1
+			} else if((param.getRead() == 0 || param.getRead() == 2) && (param.getAspect() == 0 || param.getAspect() == 1)) { //Also outputs if not paired-end since by default it is read-1 (and 5' or 3' end)
+				// Set marker (left side default, right side if positive strand and 5 prime or negative strand and 3 prime
 				int mark = sr.getUnclippedStart() - 1;
-				if(sr.getReadNegativeStrandFlag()) { 
+				if((param.getAspect() == 0 && sr.getReadNegativeStrandFlag()) || (param.getAspect() == 1 && !sr.getReadNegativeStrandFlag())) {
 					mark = sr.getUnclippedEnd() - 1;
-					mark -= SHIFT; //SHIFT DATA HERE IF NECCESSARY
-				} else { mark += SHIFT; }
+				}
+				// Shift as needed
+				if(sr.getReadNegativeStrandFlag()) { mark -= SHIFT; }
+				else { mark += SHIFT; }
+
+				//Adjust tag start to be within array reference
 				mark -= (BEDSTART - QUERYWINDOW);
 
 				//Increment Final Array keeping track of pileup

src/scripts/Read_Analysis/TagPileup.java

@@ -325,11 +325,19 @@ public String generateFileName(String bed, String bam, int strandnum) {
 		String[] bedname = bed.split("\\.");
 		String[] bamname = bam.split("\\.");
 
-		String read = "read1";
-		if (PARAM.getRead() == 1) {
-			read = "read2";
-		} else if (PARAM.getRead() == 2) {
-			read = "readc";
+		String read = "5read1";
+		if (PARAM.getAspect() == 0 && PARAM.getRead() == 1) {
+			read = "5read2";
+		} else if (PARAM.getAspect() == 0 && PARAM.getRead() == 2) {
+			read = "5readc";
+		} else if (PARAM.getAspect() == 1 && PARAM.getRead() == 0) {
+			read = "3read1";
+		} else if (PARAM.getAspect() == 1 && PARAM.getRead() == 1) {
+			read = "3read2";
+		} else if (PARAM.getAspect() == 1 && PARAM.getRead() == 2) {
+			read = "3readc";
+		} else if (PARAM.getAspect() == 2) {
+			read = "midpoint";
 		}
 
 		return (generateFileName(bedname[0] + "_" + bamname[0] + "_" + read, strandnum));