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package aligner;
import stream.Read;
public class AlignmentResult {
public AlignmentResult(int maxScore_, int maxQpos_, int maxRpos_, int qLen_, int rLen_, int rStart_, int rStop_, float ratio_) {
maxScore=maxScore_;
maxQpos=maxQpos_;
maxRpos=maxRpos_;
qLen=qLen_;
rLen=rLen_;
rStart=rStart_;
rStop=rStop_;
ratio=ratio_;
}
public int maxScore;
public int maxQpos;
public int maxRpos;
public int qLen;
public int rLen;
public int rStart;
public int rStop;
public boolean left;
public int junctionLoc;
public float ratio;
/** True if this is an ice cream cone */
public boolean icecream=false;
public boolean ambiguous=false;
public Read alignedRead;
}
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