to demo..

src/dev/java/japsadev/bio/hts/newscarf/Alignment.java

@@ -9,8 +9,11 @@
 
 public class Alignment implements Comparable<Alignment> {
 	public final static int OVERHANG_THRES=1000; 
-	
-	int score;
+	public final static int GOOD_QUAL=60; 
+
+	public static int MIN_QUAL=20; //TODO: reduce this by doing self-correction 
+
+	int alignLength, quality;
 
 	public String readID;
 	BidirectedNode node;
@@ -37,23 +40,10 @@
 	//public int readLeft, readRight, readAlign, refLeft, refRight, refAlign;
 	//left and right are in the direction of the reference sequence
 	
-	public Alignment(String readID, int refStart, int refEnd, int readLength, 
-			int readStart, int readEnd, boolean strand, boolean useful, BidirectedNode node, int score){
-		this.readID = readID;
-		this.node = node;
-		this.refStart = refStart;
-		this.refEnd = refEnd;
-		
-		this.readLength = readLength;
-		this.readStart = readStart;//1-index
-		this.readEnd = readEnd;//1-index
-		this.strand = strand;
-		this.useful = useful;			
-		this.score = score;
-	}
 	public Alignment(SAMRecord sam, BidirectedNode node) {
 //		readID = Integer.parseInt(sam.getReadName().split("_")[0]);
 		readID = sam.getReadName();
+		quality = sam.getMappingQuality();
 		prime=!sam.getNotPrimaryAlignmentFlag();
 		this.node = node;
 
@@ -104,7 +94,7 @@ public Alignment(SAMRecord sam, BidirectedNode node) {
 		int refLeft = refStart - 1;
 		int refRight = ((Sequence) node.getAttribute("seq")).length() - refEnd;
 		
-		score = refEnd + 1 - refStart;
+		alignLength = refEnd + 1 - refStart;
 		if (sam.getReadNegativeStrandFlag()){			
 			strand = false;
 			//need to convert the alignment position on read the correct direction 
@@ -118,9 +108,10 @@ public Alignment(SAMRecord sam, BidirectedNode node) {
 			)
 			goodMargin=true;
 		
-		if(		goodMargin	&&
+	if	(		goodMargin
 				//prime && //TODO: should be separated as another attribute for further consideration??
-				score > BidirectedGraph.getKmerSize() //FIXME: 
+				&& alignLength > BidirectedGraph.getKmerSize() //FIXME: 
+				&& quality >= MIN_QUAL
 			)
 			useful = true;
 

src/dev/java/japsadev/bio/hts/newscarf/BidirectedGraph.java

@@ -386,8 +386,23 @@ public static void setKmerSize(int kmer){
     	//traverse(tmp, dest, retval, distance+source.getSeq().length()+dest.getSeq().length());
     	traverse(tmp, dstNode, possiblePaths, distance, from.strand, to.strand, 0);
     	//only get the best ones
-    	if(possiblePaths.isEmpty())
-    		return null;
+    	if(possiblePaths.isEmpty()){
+    		//if a path couldn't be found between 2 dead-ends but alignments quality are insane high
+    		//FIXME: return a pseudo path having an nanopore edge
+    		if(isUnique(srcNode) && isUnique(dstNode) && srcNode.getDegree() == 1 && dstNode.getDegree()==1 &&
+				Math.min(from.quality, to.quality) >= Alignment.GOOD_QUAL)
+    		{
+    			BidirectedEdge pseudoEdge = new BidirectedEdge(srcNode, dstNode, from.strand, to.strand);
+    			//TODO: save the corresponding content of long reads to this edge
+    			pseudoEdge.setAttribute("pseudo", distance);
+    			tmp.add(pseudoEdge);
+    			retval.add(tmp);
+    			System.out.println("pseudo path from " + srcNode.getId() + " to " + dstNode.getId());
+//    			HybridAssembler.promptEnterKey();
+    			return retval;
+    		}else
+    			return null;
+    	}
     	double bestScore=possiblePaths.get(0).getDeviation();
     	for(int i=0;i<possiblePaths.size();i++){
     		BidirectedPath p = possiblePaths.get(i);

src/dev/java/japsadev/bio/hts/newscarf/GraphExplore.java

@@ -5,8 +5,8 @@
 import org.graphstream.graph.*;
 
 public class GraphExplore {
-	public static String spadesFolder="/home/sonhoanghguyen/Projects/scaffolding/data/spades_3.7/";
-	
+	//public static String spadesFolder="/home/sonhoanghguyen/Projects/scaffolding/data/spades_3.7/";
+	public static String spadesFolder="/home/hoangnguyen/workspace/data/spades/"; //sony
 	public static void main(String args[]) {
     	try {
 			new GraphExplore();
@@ -49,8 +49,8 @@ public GraphExplore() throws IOException{
         	//TODO: debug: search output for 125657_channel_96_read_33_twodimentional 
         	// assign distance to edge (not just -127 anymore but the path)
 			ass.reduceFromSPAdesPaths(spadesFolder+sample+"/contigs.paths");
-			HybridAssembler.promptEnterKey();
-			ass.assembly(spadesFolder+sample+"/assembly_graph.sam", 1);
+//			HybridAssembler.promptEnterKey();
+			ass.assembly(spadesFolder+sample+"/assembly_graph.sam");
 		} catch (IOException e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();

src/dev/java/japsadev/bio/hts/newscarf/HybridAssembler.java

@@ -38,7 +38,7 @@ public HybridAssembler(String graphFile) throws IOException{
 	}
 	
 	
-	public void assembly(String bamFile, int qual) throws IOException{
+	public void assembly(String bamFile) throws IOException{
 		SamReaderFactory.setDefaultValidationStringency(ValidationStringency.SILENT);
 
 		SamReader reader;
@@ -57,8 +57,8 @@ public void assembly(String bamFile, int qual) throws IOException{
 			SAMRecord rec = iter.next();
 			if (rec.getReadUnmappedFlag())
 				continue;
-			if (rec.getMappingQuality() < qual)
-				continue;
+//			if (rec.getMappingQuality() < qual)
+//				continue;
 			
 			String refID = rec.getReferenceName().split("_")[1];
 			Alignment myRec = new Alignment(rec, simGraph.getNode(refID)); //FIXME: optimize
@@ -249,7 +249,7 @@ public static void main(String[] argv) throws IOException{
 		//For SAM file, run bwa first on the edited assembly_graph.fastg by running:
 		//awk -F '[:;]' -v q=\' 'BEGIN{flag=0;}/^>/{if(index($1,q)!=0) flag=0; else flag=1;}{if(flag==1) print $1;}' ../EcK12S-careful/assembly_graph.fastg > Eck12-careful.fasta
 		//TODO: need to make this easier
-		hbAss.assembly(GraphExplore.spadesFolder+"bwa/EcK12S-careful.sam", 30);
+		hbAss.assembly(GraphExplore.spadesFolder+"bwa/EcK12S-careful.sam");
 	}
 	
 }

src/dev/java/japsadev/tools/NewScarfCmd.java

@@ -7,6 +7,7 @@
 
 import japsa.util.CommandLine;
 import japsa.util.deploy.Deployable;
+import japsadev.bio.hts.newscarf.Alignment;
 import japsadev.bio.hts.newscarf.BidirectedGraph;
 import japsadev.bio.hts.newscarf.HybridAssembler;
 
@@ -32,7 +33,7 @@ public static void main(String[] args) throws IOException{
 		CommandLine cmdLine = new NewScarfCmd ();
 		args = cmdLine.stdParseLine(args);
 
-		int qual = cmdLine.getIntVal("qual");
+		Alignment.MIN_QUAL = cmdLine.getIntVal("qual");
 		String fastgFile = cmdLine.getStringVal("fastg");
 		String samFile = cmdLine.getStringVal("sam");
 		String pathFile = cmdLine.getStringVal("path");
@@ -79,7 +80,7 @@ public static void main(String[] args) throws IOException{
         try {
         	if(pathFile!=null)
         		hbAss.reduceFromSPAdesPaths(pathFile);
-        	hbAss.assembly(samFile, qual);
+        	hbAss.assembly(samFile);
 		} catch (IOException e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();