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package var2;
import align2.MSA;
import dna.AminoAcid;
import shared.Shared;
import shared.Tools;
import stream.Read;
import stream.SamLine;
import stream.SiteScore;
public class Realigner {
public Realigner(){
this(defaultMaxrows, defaultColumns, defaultPadding, defaultMsaType);
}
public Realigner(int maxrows_, int columns_, int padding_, String msaType_){
maxrows=maxrows_;
columns=columns_;
padding=padding_;
msaType=msaType_;
msa=MSA.makeMSA(maxrows, columns+2, msaType);
}
public boolean realign(Read r, SamLine sl, final boolean unclip){
if(!r.mapped() || sl.supplementary() || !sl.primary()){return false;}
Scaffold scaf=map.getScaffold(sl.rnameS());
assert(scaf!=null) : sl.rnameS();
return realign(r, sl, scaf, unclip);
}
public boolean realign(final Read r, final SamLine sl, final Scaffold scaf, final boolean unclip){
return realign(r, sl, scaf.bases, unclip);
}
public boolean realign(final Read r, final SamLine sl, final byte[] ref, final boolean unclip){
if(!r.mapped() || sl.supplementary() || !sl.primary()){return false;}
int[] mSCNID=r.countMatchSymbols();
int sumBad=mSCNID[1]+mSCNID[4]+mSCNID[5], sumIndel=mSCNID[4]+mSCNID[5];
if(mSCNID[2]>0){//continue
}else if(sumBad>3){//continue
}else if(sumIndel>1 || (sumIndel>0 && mSCNID[1]>1)){//continue
}else{return false;}
if(mSCNID[1]<3 && mSCNID[2]==0 && mSCNID[4]<2 && mSCNID[5]<2 && sumBad<3 && sumIndel<2){return false;}
if(r.length()+2>msa.maxColumns+2*padding){
msa=MSA.makeMSA(msa.maxRows, r.length()+2+r.length()/4+2*padding, msaType);
}
if(r.length()+2>msa.maxRows){
msa=MSA.makeMSA(r.length()+2+r.length()/4+2*padding, msa.maxColumns, msaType);
}
final int leadingClip=SamLine.countLeadingClip(sl.cigar, true, false);
final int trailingClip=SamLine.countTrailingClip(sl.cigar, true, false);
final int totalClip=leadingClip+trailingClip;
final boolean clipped=totalClip>0;
final int start=sl.start(true, false);
final int stop=sl.stop(start, true, false);
final int paddedStart=start-padding, paddedStop=stop+padding;
final int len0=paddedStop-paddedStart+1;
final int a=0, b=len0-1;
if(len0>=columns){return false;}
realignmentsAttempted++;
SiteScore ss=null;
final byte[] rbases=makeRbases(ref, start, stop, padding);
byte[] qbases=r.bases;
if(sl.strand()==Shared.MINUS){
qbases=AminoAcid.reverseComplementBases(qbases);
}
// SiteScore oldSS=r.toSite(); //123 Slow
// oldSS.match=r.match.clone(); //123 Slow
// String oldSL=sl.toString(); //123 Slow
// assert(oldSS.lengthsAgree()) : oldSS.start+", "+oldSS.stop+", "+oldSS.matchLength()+", "+oldSS.mappedLength()+", "+scaf.length+"\n"+sl+"\n"+oldSS+"\n";
// assert(!oldSS.matchContainsXY()) : oldSS.start+", "+oldSS.stop+", "+oldSS.matchLength()+", "+oldSS.mappedLength()+", "+scaf.length+"\n"+sl+"\n"+oldSS+"\n";
assert(!r.shortmatch()); //Otherwise convert it or change the score function.
final int score0=msa.score(r.match);
final int minScore=clipped ? 1 : Tools.max(1, score0-1);
final int[] max;
max=msa.fillLimited(qbases, rbases, a, b, minScore, null);
if(max==null){return false;}
final int[] score=msa.score(qbases, rbases, a, b, max[0], max[1], max[2], false);
if(score==null){return false;}
realignmentsSucceeded++;
if(score[0]<=minScore || (score[0]<=score0 && !clipped)){return false;}
realignmentsImproved++;
// assert(false) : score[0]+", "+minScore+", "+score0;
ss=new SiteScore(1, r.strand(), score[1], score[2], 1, score[0]);
ss.setSlowScore(ss.quickScore);
ss.score=ss.quickScore;
ss.match=msa.traceback(qbases, rbases, a, b, score[3], score[4], score[5], false);
assert(ss.match!=null);
SiteScore oldSS2=ss.clone(); //123 Slow
oldSS2.match=ss.match.clone(); //123 Slow
// assert(ss.lengthsAgree()) : ss.start+", "+ss.stop+", "+ss.matchLength()+", "+ss.mappedLength()+", "+scaf.length+"\n"+sl+"\n"+ss+"\n"
// +oldSS.start+", "+oldSS.stop+", "+oldSS.matchLength()+", "+oldSS.mappedLength()+", "+scaf.length+"\n"+sl+"\n"+oldSS+"\n"
// ;
// assert(!oldSS.matchContainsXY()) : ss.start+", "+ss.stop+", "+ss.matchLength()+", "+ss.mappedLength()+", "+scaf.length+"\n"+sl+"\n"+ss+"\n"
// +oldSS.start+", "+oldSS.stop+", "+oldSS.matchLength()+", "+oldSS.mappedLength()+", "+scaf.length+"\n"+sl+"\n"+oldSS+"\n"
// ;
//These pass
// assert(sl.strand()==ss.strand()) : sl.strand()+", "+ss.strand()+", "+r.strand()+", "+oldSS.strand()+", "+oldSS2.strand();
// assert(sl.strand()==r.strand());
// assert(sl.strand()==oldSS.strand());
// assert(sl.strand()==oldSS2.strand());
// SiteScore old=r.toSite();
//Correct for adjusted ref
ss.start=ss.start+paddedStart;
ss.stop=ss.stop+paddedStart;
{
int clipped2=ss.clipTipIndels(ref.length);
if(unclip && clipped2>0 && ref!=null && oldSS2.match[oldSS2.match.length-1]=='Y'){
ss.unclip(qbases, ref);
// System.err.println(sl.strand()+"\n"+new String(new String(oldSS2.match)+"\n"+new String(ss.match)));
}
}
if(ss.matchContainsXY()){return false;}
if(ss.matchContainsAB()){return false;}
realignmentsRetained++;
r.start=ss.start;
r.stop=ss.stop;
// System.err.println("old:\t"+old+"\nnew:\t"+ss+"\nold score:"+score0+"\n");
// assert(false);
r.match=ss.match;
sl.pos=Tools.max(0, r.start)+1;
sl.cigar=SamLine.toCigar14(r.match, r.start, r.stop, ref.length, qbases);
sl.optional=null;
// assert((ss.start>=0) == (SamLine.countLeadingClip(sl.cigar, true, true)==0)) : ss.start+", "+ss.stop+", "+scaf.length+"\n"+sl+"\n"+ss+"\n"
// +oldSL+"\n"+oldSS+"\n"+oldSS2+"\n"
// ;
// assert((ss.stop<scaf.length) == (SamLine.countTrailingClip(sl.cigar, true, true)==0)) : ss.start+", "+ss.stop+", "+scaf.length+"\n"+sl+"\n"
// +oldSL+"\n"+oldSS+"\n"+oldSS2+"\n"
// ;
// assert((ss.start>=0) || (SamLine.countLeadingClip(sl.cigar, true, true)>0)) : ss.start+", "+ss.stop+", "+scaf.length+"\n"+sl+"\n"+ss+"\n"
// +oldSL+"\n"+oldSS+"\n"+oldSS2+"\n"
// ;
// assert((ss.stop<scaf.length) || (SamLine.countTrailingClip(sl.cigar, true, true)>0)) : ss.start+", "+ss.stop+", "+scaf.length+"\n"+sl+"\n"
// +oldSL+"\n"+oldSS+"\n"+oldSS2+"\n"
// ;
//Perform clipping
r.match=SamLine.cigarToShortMatch_old(sl.cigar, true);
r.setShortMatch(true);
r.toLongMatchString(true);
return true;
}
private static byte[] makeRbases(byte[] bases, int start, int stop, int padding) {
final int start2=start-padding, stop2=stop+padding;
byte[] out=new byte[stop2-start2+1];
for(int opos=0, bpos=start2; opos<out.length; opos++, bpos++){
byte b=(bpos<0 || bpos>=bases.length ? (byte)'N' : bases[bpos]);
out[opos]=b;
}
return out;
}
public MSA msa(){return msa;}
long realignmentsAttempted=0;
long realignmentsSucceeded=0;
long realignmentsRetained=0;
long realignmentsImproved=0;
private int maxrows=602;
private int columns=2000;
private int padding=100;
private String msaType;
private MSA msa;
public static int defaultMaxrows=603;
public static int defaultColumns=2000;
public static int defaultPadding=200;
public static String defaultMsaType="MultiStateAligner11ts";
public static ScafMap map=null;
}
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