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package var2;
import shared.Parse;
import shared.Shared;
import shared.Tools;
import stream.SamLine;
import structures.CoverageArray;
import structures.CoverageArray2;
import structures.CoverageArray3;
import structures.CoverageArray3A;
public class Scaffold {
/** Assumes SAM format.
* e.g.<br> @SQ SN:scaffold_0 LN:1785514 AS:build 9 */
public Scaffold(byte[] line, int scafnum){
assert(Tools.startsWith(line, "@SQ\t")) : new String(line);
number=scafnum;
int a=0, b=0;
while(b<line.length && line[b]!='\t'){b++;}
assert(b>a) : "Missing field 0: "+new String(line);
b++;
a=b;
while(b<line.length && line[b]!='\t'){b++;}
assert(b>a) : "Missing field 1: "+new String(line);
assert(Tools.startsWith(line, "SN:", a));
name=new String(line, a+3, b-a-3);
b++;
a=b;
while(b<line.length && line[b]!='\t'){b++;}
assert(b>a) : "Missing field 2: "+new String(line);
assert(Tools.startsWith(line, "LN:", a));
length=Parse.parseInt(line, a+3, b);
b++;
a=b;
}
public Scaffold(String name_, int scafnum_, int len_){
name=name_;
number=scafnum_;
length=len_;
}
public void add(SamLine sl){
int start=sl.pos-1;
int stop=sl.stop(start, false, false);
increment(start, stop, sl.strand());
}
public void increment(int from, int to, int strand){
// assert(trackStrand);
if(!initialized()){
synchronized(this){
if(!initialized()){
// assert(ca==null);
// assert(caMinus==null);
// assert(trackStrand);
ca=useCA3A ? new CoverageArray3A(number, length) : useCA3 ? new CoverageArray3(number, length) : new CoverageArray2(number, length);
if(trackStrand){
caMinus=useCA3A ? new CoverageArray3A(number, length) : useCA3 ? new CoverageArray3(number, length) : new CoverageArray2(number, length);
}
}
initialized=true;
}
// assert(ca!=null);
// assert(!trackStrand || caMinus!=null) : trackStrand;
}
assert(initialized());
assert(ca!=null);
// assert(!trackStrand || caMinus!=null) : trackStrand;
// assert(trackStrand);
ca.incrementRangeSynchronized(from, to, 1);
if(trackStrand && strand==Shared.MINUS){caMinus.incrementRangeSynchronized(from, to, 1);}
}
public synchronized void incrementOld(int from, int to, int strand){
if(ca==null){
ca=useCA3 ? new CoverageArray3(number, length) : new CoverageArray2(number, length);
}
ca.incrementRange(from, to);
if(trackStrand && strand==Shared.MINUS){
if(caMinus==null){
caMinus=useCA3 ? new CoverageArray3(number, length) : new CoverageArray2(number, length);
}
caMinus.incrementRange(from, to);
}
}
public String getSequence(SamLine sl) {
int start=sl.start(false, false);
int stop=sl.stop(start, false, false);
return getSequence(start, stop);
}
public String getSequence(int start, int stop) {
assert(bases!=null) : this;
start=Tools.max(0, start);
stop=Tools.min(bases.length-1, stop);
String s=new String(bases, start, stop-start+1);
return s;
}
public int calcCoverage(Var v){
return calcCoverage(v, ca);
}
public int minusCoverage(Var v){
assert(trackStrand);
return calcCoverage(v, caMinus);
}
public int calcCoverage(Var v, CoverageArray ca){
final int a=v.start;
final int b=v.stop;
// assert(false) : ca.maxIndex+", "+a;
if(ca==null || ca.maxIndex<a){return 0;}
final int type=v.type();
final int avg;
final int rlen=v.reflen();
long sum=0;
if(type==Var.SUB || type==Var.NOCALL || type==Var.DEL){
for(int i=a; i<b; i++){
sum+=ca.get(i);
}
avg=(int)Math.round(sum/(double)rlen);
}else if(type==Var.INS){
assert(rlen==0 && a==b);
// if(a<=0){sum=2*ca.get(0);}
// else if(b>ca.maxIndex)
if(b>=ca.maxIndex){
sum=2*ca.get(ca.maxIndex);
avg=(int)(sum/2);
}else{
sum=ca.get(a)+ca.get(b);
avg=(int)Math.ceil(sum/2);
}
}else if(type==Var.LJUNCT){
//Take coverage from right of junction, unless that's off the end.
//but it should be impossible for that to be off the end.
avg=ca.get(Tools.min(ca.maxIndex, a+1));
}else if(type==Var.RJUNCT){
//Take coverage from left of junction, unless that's off the end.
//but it should be impossible for that to be off the end.
avg=ca.get(Tools.max(0, a-1));
}else{
throw new RuntimeException("Unknown type "+type+"\n"+v);
}
return avg;
}
@Override
public String toString(){
return "@SQ\tSN:"+name+"\tLN:"+length+"\tID:"+number;
}
public synchronized void clearCoverage(){
ca=null;
caMinus=null;
initialized=false;
}
public final String name;
public final int number;
public final int length;
private CoverageArray ca;
private CoverageArray caMinus;
public byte[] bases;
private boolean initialized(){return initialized;};
private boolean initialized;
public static void setCA3(boolean b){useCA3=b;}
public static void setCA3A(boolean b){useCA3A=b;}
public static void setTrackStrand(boolean b){trackStrand=b;}
public static boolean trackStrand(){return trackStrand;}
private static boolean useCA3=false;
private static boolean useCA3A=true;
private static boolean trackStrand=false;
}
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