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package hiseq;
import dna.AminoAcid;
import shared.Tools;
import stream.Read;
import structures.ByteBuilder;
public class MicroTile {
public MicroTile(){}
public MicroTile(int lane_, int tile_, int x1_, int x2_, int y1_, int y2_){
lane=lane_;
tile=tile_;
x1=x1_;
x2=x2_;
y1=y1_;
y2=y2_;
}
void process(){
if(tracker!=null){tracker.process();}
}
public boolean contains(int x, int y){
return x>=x1 && x<=x2 && y>=y1 && y<=y2;
}
@Override
public String toString(){
return lane+", "+tile+", "+x1+", "+x2+", "+y1+", "+y2;
}
public double averageQuality(){
return readCount==0 ? 0 : qualitySum/readCount;
}
public double percentErrorFree(){
return readCount==0 ? 0 : errorFreeSum/readCount;
}
public double hitPercent(){
long count=kmerCount();
return count==0 ? 0 : hits*100.0/count;
}
public double uniquePercent(){
long count=kmerCount();
return count==0 ? 0 : misses*100.0/count;
}
public double avgG(){
return tracker==null ? 0 : tracker.avg('G');
}
public double maxG(){
return tracker==null ? 0 : tracker.max('G');
}
public long kmerCount(){return hits+misses;}
public void add(MicroTile mt) {
hits+=mt.hits;
misses+=mt.misses;
readCount+=mt.readCount;
qualitySum+=mt.qualitySum;
errorFreeSum+=mt.errorFreeSum;
for(int i=0; i<acgtn.length; i++){
acgtn[i]+=mt.acgtn[i];
}
homoPolyGCount+=mt.homoPolyGCount;
homoPolyGSum+=mt.homoPolyGSum;
if(TRACK_CYCLES){
tracker.add(mt.tracker);
}
}
public void add(Read r){
if(r==null){return;}
final int len=r.length();
if(len<1){return;}
readCount++;
qualitySum+=r.avgQualityByProbabilityDouble(true, len);
errorFreeSum+=100*r.probabilityErrorFree(true, len);
final byte[] bases=r.bases;
int maxPolyG=0, currentPolyG=0;
for(int i=0; i<len; i++){
byte b=bases[i];
byte x=AminoAcid.baseToNumberACGTN[b];
acgtn[x]++;
if(b=='G'){
currentPolyG++;
maxPolyG=Tools.max(currentPolyG, maxPolyG);
}else{
currentPolyG=0;
}
}
homoPolyGCount+=(maxPolyG>=MIN_POLY_G ? 1 : 0);
homoPolyGSum+=maxPolyG;
if(TRACK_CYCLES){
tracker.add(r);
}
}
public void toText(ByteBuilder bb){
bb.append(lane).append('\t');
bb.append(tile).append('\t');
bb.append(x1).append('\t');
bb.append(x2).append('\t');
bb.append(y1).append('\t');
bb.append(y2).append('\t');
bb.append(readCount).append('\t');
bb.append(uniquePercent(), 3).append('\t');
bb.append(averageQuality(), 3).append('\t');
bb.append(percentErrorFree(), 3).append('\t');
bb.append(discard);
for(int i=0; i<5; i++){
bb.tab().append(acgtn[i]);
}
bb.tab().append(homoPolyGCount);
bb.tab().append(homoPolyGSum);
bb.nl();
}
public long hits;
public long misses;
public long readCount;
public double qualitySum;
public double errorFreeSum;
public int discard=0;
public int lane;
public int tile;
public int x1, x2;
public int y1, y2;
//TODO: These fields are not currently parsed.
public long[] acgtn=new long[5];
public long homoPolyGCount;
public long homoPolyGSum;
public final CycleTracker tracker=TRACK_CYCLES ? new CycleTracker() : null;
public static int MIN_POLY_G=25;
public static boolean TRACK_CYCLES=false;
}
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