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package aligner;
import prok.GeneCaller;
import shared.Tools;
import stream.Read;
import structures.ByteBuilder;
import structures.LongHashMap;
/**
* Aligns reads to a small, single sequence reference like PhiX.
* The reference should not have any duplicate kmers.
* Alignment is only attempted once, at the first matching kmer.
* This will generate a match string and return the identity.
* Mapped reads can be printed as sam output.
*
* @author Brian Bushnell
* @date November 15, 2024
*
*/
public class MicroAligner3 implements MicroAligner {
/*--------------------------------------------------------------*/
/*---------------- Initialization ----------------*/
/*--------------------------------------------------------------*/
public MicroAligner3(MicroIndex3 index_, float minIdentity_, boolean shared_) {
index=index_;
minIdentity=minIdentity_;
maxSubFraction=1-minIdentity;
k=index.k;
k2=k-1;
middleMask=index.middleMask;
shared=shared_;
myBuffer=(shared ? null : new ByteBuilder());
mySSA=(shared ? null : new SingleStateAlignerFlat2());
}
/*--------------------------------------------------------------*/
/*---------------- Alignment ----------------*/
/*--------------------------------------------------------------*/
/** Returns identity */
public float map(Read r) {
return map(r, minIdentity);
}
/** Returns identity */
public float map(Read r, float minid) {
if(r==null || r.length()<k || r.match!=null || r.samline!=null) {return 0;}
final long ret=index.map(r);
if(ret==index.NO_HIT) {
assert(!r.mapped());
return 0;
}
int strand=(int)(ret&1);
int offset=(int)(ret>>1);
assert(offset==r.start);
final float id;
int pad=5;
if(strand==1) {
r.reverseComplement();
id=align(r, index.ref, offset, offset+r.length(), pad, minid);
r.reverseComplement();
if(r.mapped()) {r.setStrand(1);}
}else {
id=align(r, index.ref, offset, offset+r.length(), pad, minid);
}
assert(id>=minid || !r.mapped()) : "\nid="+id+"<"+minid+"\n"+r+"\n"+r.mate.toFastq()+"\n";
return id;
}
public float align(Read r, byte[] ref, int a, int b, int pad, float minid){
assert(!r.mapped());
{
final float id=quickAlign(r, ref, a, minid);
if(id>minid) {
assert(r.mapped());
return id;
}
}
assert(!r.mapped());
SingleStateAlignerFlat2 ssa=getSSA();
a=Tools.max(0, a-pad);
b=Tools.min(ref.length-1, b+pad);
int[] max=ssa.fillUnlimited(r.bases, ref, a, b, 0);
if(max==null){return 0;}
final int rows=max[0];
final int maxCol=max[1];
final int maxState=max[2];
//returns {score, bestRefStart, bestRefStop}
//padded: {score, bestRefStart, bestRefStop, padLeft, padRight};
int[] score=ssa.score(r.bases, ref, a, b, rows, maxCol, maxState);
int rstart=score[1];
int rstop=score[2];
r.start=rstart;
r.stop=rstop;
r.chrom=1;
final byte[] match=ssa.traceback(r.bases, ref, a, b, rows, maxCol, maxState);
final float id=Read.identity(match);
if(id<minid) {return id;}//Probably not phix
r.setMapped(true);
r.match=match;
assert(id>=minid || !r.mapped()) : "\nid="+id+"<"+minid+"\n"+r+"\n"+r.mate.toFastq()+"\n";
return id;
}
/** Returns identity (approx, in the case of Ns) */
public float quickAlign(Read read, byte[] ref, int a, float minid) {
byte[] bases=read.bases;
ByteBuilder buffer=getBuffer();
buffer.clear();
int subs=0, ns=0;
for(int i=0, j=a; i<bases.length; i++, j++) {
if(j<0 || j>=ref.length) {
buffer.append('C');
}else {
final byte q=bases[i], r=ref[j];
if(q=='N') {
buffer.append('N');
ns++;
}else if(r=='N' || r==q) {
buffer.append('m');
}else {
buffer.append('S');
subs++;
}
}
}
int matches=bases.length-subs-ns;
if(subs>3 || matches*4<bases.length) {return 0;}
float id=(subs+ns*0.0625f)/Tools.max(1f, matches+0.25f*ns+subs);
if(id>=minid) {
read.match=buffer.toBytes();
read.start=a;
read.stop=a+read.length()-1;
read.chrom=1;
read.setMapped(true);
}
return id;
}
/*--------------------------------------------------------------*/
/*---------------- Getters ----------------*/
/*--------------------------------------------------------------*/
private final SingleStateAlignerFlat2 getSSA() {
if(!shared) {return mySSA;}
return GeneCaller.getSSA();
}
private final ByteBuilder getBuffer() {
if(!shared) {return myBuffer;}
return buffer();
}
private static final ByteBuilder buffer() {
ByteBuilder buffer=bufferHolder.get();
if(buffer==null) {
buffer=new ByteBuilder();
bufferHolder.set(buffer);
}
return buffer;
}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
public LongHashMap getMap() {return index.map;}
final float minIdentity;
final float maxSubFraction;
final int k;
final int k2;
final long middleMask;
final MicroIndex3 index;
final SingleStateAlignerFlat2 mySSA;
final ByteBuilder myBuffer;
final boolean shared;
/*--------------------------------------------------------------*/
/*---------------- Statics ----------------*/
/*--------------------------------------------------------------*/
private static final float nMult=1024;
private static final float nMultInv=1.0f/nMult;
private static final ThreadLocal<ByteBuilder> bufferHolder=new ThreadLocal<ByteBuilder>();
// final ByteBuilder buffer=new ByteBuilder();
}
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