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