jpayne@68: package icecream;
jpayne@68: 
jpayne@68: import stream.Read;
jpayne@68: import structures.ByteBuilder;
jpayne@68: 
jpayne@68: class ReadBuilder {
jpayne@68: 	
jpayne@68: 	public ReadBuilder(byte[] bases_, float passes_, int movieStart_, long zmw_) {
jpayne@68: 		this(new ByteBuilder(bases_), passes_, movieStart_, zmw_);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public ReadBuilder(ByteBuilder bases_, float passes_, int movieStart_, long zmw_) {
jpayne@68: 		bases=bases_;
jpayne@68: 		passes=passes_;
jpayne@68: 		movieStart=movieStart_;
jpayne@68: 		movieStop=movieStart+bases.length();
jpayne@68: 		zmw=zmw_;
jpayne@68: 
jpayne@68: 		fullPasses=passes<1 ? 0 : 1;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static boolean isIceCream(String id){
jpayne@68: 		String[] terms=id.split("\t");
jpayne@68: 		int subreads=Integer.parseInt(terms[3].split("=")[1]);
jpayne@68: 		return subreads>1;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static ReadBuilder parse(Read r) {
jpayne@68: 		ByteBuilder bases=new ByteBuilder(r.bases);
jpayne@68: 		String[] terms=r.id.split("\t");
jpayne@68: 		String[] name=terms[0].split("/");
jpayne@68: 		String[] position=name[2].split("_");
jpayne@68: 		
jpayne@68: 		int movieStart=Integer.parseInt(position[0]);
jpayne@68: 		int movieStop=Integer.parseInt(position[1]);
jpayne@68: 		long zmw=Long.parseLong(name[1]);
jpayne@68: 		
jpayne@68: 		float passes=Float.parseFloat(terms[1].split("=")[1]);
jpayne@68: 		int fullPasses=Integer.parseInt(terms[2].split("=")[1]);
jpayne@68: 		int subreads=Integer.parseInt(terms[3].split("=")[1]);
jpayne@68: 		int missing=Integer.parseInt(terms[4].split("=")[1]);
jpayne@68: 		int adapters=Integer.parseInt(terms[5].split("=")[1]);
jpayne@68: 		float errorRate=(terms.length<7 ? 0 : Float.parseFloat(terms[6].split("=")[1]));
jpayne@68: 		
jpayne@68: 		ReadBuilder rb=new ReadBuilder(bases, passes, movieStart, zmw);
jpayne@68: 		rb.movieStop=movieStop;
jpayne@68: 		rb.passes=passes;
jpayne@68: 		rb.fullPasses=fullPasses;
jpayne@68: 		rb.subreads=subreads;
jpayne@68: 		rb.missing=missing;
jpayne@68: 		rb.adapters=adapters;
jpayne@68: 		rb.errorRate=errorRate;
jpayne@68: 		return rb;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public String toString(){
jpayne@68: 		return toHeader().toString();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public ByteBuilder toHeader(){
jpayne@68: 		ByteBuilder id=new ByteBuilder(200);
jpayne@68: 		id.append("m1_2_3/");
jpayne@68: 		id.append(zmw).append('/').append(movieStart).append('_').append(movieStop);
jpayne@68: 		id.tab().append("passes=").append(passes, 2);
jpayne@68: 		id.tab().append("fullPasses=").append(fullPasses);
jpayne@68: 		id.tab().append("subreads=").append(subreads);
jpayne@68: 		id.tab().append("missing=").append(missing);
jpayne@68: 		id.tab().append("adapters=").append(adapters);
jpayne@68: 		id.tab().append("errorRate=").append(errorRate, 3);
jpayne@68: 		return id;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public int length() {
jpayne@68: 		return bases.length();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void add(ReadBuilder rb){
jpayne@68: 		bases.append(rb.bases);
jpayne@68: 		
jpayne@68: 		movieStop+=rb.length();
jpayne@68: 		missing+=rb.missing;
jpayne@68: 		adapters+=rb.adapters;
jpayne@68: 		fullPasses+=rb.fullPasses;
jpayne@68: 		subreads+=rb.subreads;
jpayne@68: 		passes+=rb.passes;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	Read toRead() {
jpayne@68: 		//Example: m54283_190403_183820/4194374/919_2614
jpayne@68: 		//Run ID is m54283_190403_183820
jpayne@68: 		//zmw ID is 4194374.
jpayne@68: 		//Read start/stop coordinates are 919_2614
jpayne@68: 		
jpayne@68: 		ByteBuilder id=toHeader();
jpayne@68: 		Read r=new Read(bases.toBytes(), null, id.toString(), 0);
jpayne@68: 		return r;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	ByteBuilder bases;
jpayne@68: 
jpayne@68: 	final long zmw;
jpayne@68: 	final int movieStart;
jpayne@68: 	int movieStop;
jpayne@68: 	
jpayne@68: 	float passes;
jpayne@68: 	int fullPasses=0;
jpayne@68: 	int subreads=1;
jpayne@68: 	int missing=0;
jpayne@68: 	int adapters=0;
jpayne@68: 	float errorRate=0;
jpayne@68: }