package align2;

import java.util.ArrayList;
import java.util.Arrays;

import bloom.BloomFilter;
import dna.AminoAcid;
import dna.ChromosomeArray;
import dna.Data;
import jgi.CoveragePileup;
import shared.ReadStats;
import shared.Shared;
import shared.Tools;
import shared.TrimRead;
import stream.ConcurrentReadInputStream;
import stream.ConcurrentReadOutputStream;
import stream.Read;
import stream.SamLine;
import stream.SiteScore;
import structures.ListNum;
import structures.LongList;



/**
 * @author Brian Bushnell
 * @date Feb 27, 2013
 *
 */
public abstract class AbstractMapThread extends Thread {
	
	AbstractMapThread(ConcurrentReadInputStream cris_,
			ConcurrentReadOutputStream outStream_, ConcurrentReadOutputStream outStreamMapped_, ConcurrentReadOutputStream outStreamUnmapped_, ConcurrentReadOutputStream outStreamBlack_,
			CoveragePileup pileup_, boolean SLOW_ALIGN_, boolean LOCAL_ALIGN_, boolean AMBIGUOUS_TOSS_,
			boolean AMBIGUOUS_RANDOM_, boolean AMBIGUOUS_ALL_, boolean TRIM_LEFT_, boolean TRIM_RIGHT_, boolean UNTRIM_, float TRIM_QUAL_, int MIN_TRIM_LEN_, int THRESH_,
			int minChrom_, int maxChrom_, int KFILTER_, float IDFILTER_, boolean KILL_BAD_PAIRS_, boolean SAVE_AMBIGUOUS_XY_,
			boolean REQUIRE_CORRECT_STRANDS_PAIRS_,
			boolean SAME_STRAND_PAIRS_, boolean DO_RESCUE_, boolean STRICT_MAX_INDEL_, int SLOW_ALIGN_PADDING_, int SLOW_RESCUE_PADDING_,
			String MSA_TYPE_, int keylen_, boolean PERFECTMODE_, boolean SEMIPERFECTMODE_, boolean FORBID_SELF_MAPPING_, boolean RCOMP_MATE_,
			boolean MAKE_MATCH_STRING_, boolean OUTPUT_MAPPED_ONLY_, boolean DONT_OUTPUT_BLACKLISTED_READS_, boolean PRINT_SECONDARY_ALIGNMENTS_,
			boolean QUICK_MATCH_STRINGS_, int MAX_SITESCORES_TO_PRINT_, float MINIMUM_ALIGNMENT_SCORE_RATIO_,
			float keyDensity_, float maxKeyDensity_, float minKeyDensity_, int maxDesiredKeys_,
			int MIN_APPROX_HITS_TO_KEEP_, boolean USE_EXTENDED_SCORE_, int BASE_HIT_SCORE_, boolean USE_AFFINE_SCORE_, int MAX_INDEL_,
			boolean TRIM_LIST_, int TIP_DELETION_SEARCH_RANGE_, BloomFilter bloomFilter_){
		
		
		cris=cris_;
		outStream=outStream_;
		outStreamMapped=outStreamMapped_;
		outStreamUnmapped=outStreamUnmapped_;
		outStreamBlack=outStreamBlack_;
		pileup=pileup_;
		
		SLOW_ALIGN=SLOW_ALIGN_;
		LOCAL_ALIGN=LOCAL_ALIGN_;
		AMBIGUOUS_TOSS=AMBIGUOUS_TOSS_;
		AMBIGUOUS_RANDOM=AMBIGUOUS_RANDOM_;
		AMBIGUOUS_ALL=AMBIGUOUS_ALL_;
		TRIM_LEFT=TRIM_LEFT_;
		TRIM_RIGHT=TRIM_RIGHT_;
		UNTRIM=UNTRIM_;
		TRIM_QUAL=TRIM_QUAL_;
		TRIM_ERROR_RATE=(float)QualityTools.phredToProbError(TRIM_QUAL);
		TRIM_MIN_LENGTH=MIN_TRIM_LEN_;
		THRESH=THRESH_;
		minChrom=minChrom_;
		maxChrom=maxChrom_;
		KFILTER=KFILTER_;
		IDFILTER=IDFILTER_;
		RenameByInsert=AbstractMapper.RenameByInsert;
		
		KILL_BAD_PAIRS=KILL_BAD_PAIRS_;
		SAVE_AMBIGUOUS_XY=SAVE_AMBIGUOUS_XY_;
//		GEN_MATCH_FAST=GEN_MATCH_FAST_;
		SLOW_ALIGN_PADDING=SLOW_ALIGN_PADDING_;
		SLOW_RESCUE_PADDING=SLOW_RESCUE_PADDING_;
		DO_RESCUE=DO_RESCUE_;
		STRICT_MAX_INDEL=STRICT_MAX_INDEL_;
		BANDWIDTH=MSA.bandwidth;
		PAIRED=cris.paired();
		REQUIRE_CORRECT_STRANDS_PAIRS=REQUIRE_CORRECT_STRANDS_PAIRS_;
		SAME_STRAND_PAIRS=SAME_STRAND_PAIRS_;
		
		/* ------------ */
		
		TRIM_LIST=TRIM_LIST_;
		TIP_DELETION_SEARCH_RANGE=TIP_DELETION_SEARCH_RANGE_;
		FIND_TIP_DELETIONS=TIP_DELETION_SEARCH_RANGE>0;
		
		MIN_APPROX_HITS_TO_KEEP=MIN_APPROX_HITS_TO_KEEP_;
		USE_EXTENDED_SCORE=USE_EXTENDED_SCORE_;
		BASE_HIT_SCORE=BASE_HIT_SCORE_;
		BASE_KEY_HIT_SCORE=BASE_HIT_SCORE*keylen_;
		USE_AFFINE_SCORE=USE_AFFINE_SCORE_;
		EXPECTED_LEN_LIMIT=(ALIGN_COLUMNS()*17)/20-(2*(SLOW_ALIGN_PADDING+10)); //TODO: Due to some bug in expected length calculation, this is low.
		MAX_INDEL=MAX_INDEL_;
		ALIGN_COLUMNS_ABSTRACT=ALIGN_COLUMNS();
		
		/* ------------ */
		
		
		KEYLEN=keylen_;
		keyDensity=keyDensity_;
		maxKeyDensity=maxKeyDensity_;
		minKeyDensity=minKeyDensity_;
		maxDesiredKeys=maxDesiredKeys_;
		
		MINIMUM_ALIGNMENT_SCORE_RATIO=MINIMUM_ALIGNMENT_SCORE_RATIO_;
		MINIMUM_ALIGNMENT_SCORE_RATIO_PAIRED=Tools.max(MINIMUM_ALIGNMENT_SCORE_RATIO*.80f, 1-((1-MINIMUM_ALIGNMENT_SCORE_RATIO)*1.4f));
		MINIMUM_ALIGNMENT_SCORE_RATIO_PRE_RESCUE=Tools.max(MINIMUM_ALIGNMENT_SCORE_RATIO*.60f,  1-((1-MINIMUM_ALIGNMENT_SCORE_RATIO)*1.8f));
//		TRIM_LIST=TRIM_LIST_;
		MAKE_MATCH_STRING=(MAKE_MATCH_STRING_ || STRICT_MAX_INDEL_);
		assert(SLOW_ALIGN_PADDING>=0);
		
		OUTPUT_MAPPED_ONLY=OUTPUT_MAPPED_ONLY_;
		DONT_OUTPUT_BLACKLISTED_READS=DONT_OUTPUT_BLACKLISTED_READS_;
		MAX_SITESCORES_TO_PRINT=MAX_SITESCORES_TO_PRINT_;
		PRINT_SECONDARY_ALIGNMENTS=PRINT_SECONDARY_ALIGNMENTS_;
		QUICK_MATCH_STRINGS=((QUICK_MATCH_STRINGS_ || STRICT_MAX_INDEL_) && MAKE_MATCH_STRING);
		
		RCOMP_MATE=RCOMP_MATE_;
		PERFECTMODE=PERFECTMODE_;
		SEMIPERFECTMODE=SEMIPERFECTMODE_;
		FORBID_SELF_MAPPING=FORBID_SELF_MAPPING_;
//		assert(!(RCOMP_MATE/* || FORBID_SELF_MAPPING*/)) : "RCOMP_MATE: TODO";
		
//		TIP_DELETION_SEARCH_RANGE=TIP_DELETION_SEARCH_RANGE_;
//		FIND_TIP_DELETIONS=TIP_DELETION_SEARCH_RANGE>0;
//		EXPECTED_LEN_LIMIT=(ALIGN_COLUMNS*17)/20-(2*(SLOW_ALIGN_PADDING+10)); //TODO: Due to some bug in expected length calculation, this is low.
		MSA_TYPE=MSA_TYPE_;
		EXTRA_PADDING=(BANDWIDTH<1 && (MSA.bandwidthRatio<=0 || MSA.bandwidthRatio>=0.2f) ?
				EXTRA_PADDING : Tools.min(EXTRA_PADDING, Tools.max(BANDWIDTH/4, (int)(MSA.bandwidthRatio*60))));
		
		AVERAGE_PAIR_DIST=INITIAL_AVERAGE_PAIR_DIST;
		
		if(SLOW_ALIGN || MAKE_MATCH_STRING){
			msa=MSA.makeMSA(ALIGN_ROWS(), ALIGN_COLUMNS(), MSA_TYPE);
			POINTS_MATCH=msa.POINTS_MATCH();
			POINTS_MATCH2=msa.POINTS_MATCH2();
//			CLEARZONE1=(int)(CLEARZONE_RATIO1*POINTS_MATCH2);
//			CLEARZONE1b=(int)(CLEARZONE_RATIO1b*POINTS_MATCH2);
//			CLEARZONE1c=(int)(CLEARZONE_RATIO1c*POINTS_MATCH2);
//			CLEARZONEP=(int)(CLEARZONE_RATIOP*POINTS_MATCH2);
//			CLEARZONE3=PENALIZE_AMBIG ? (int)(CLEARZONE_RATIO3*POINTS_MATCH2) : 0;
			CLEARZONE1e=2*POINTS_MATCH2-POINTS_MATCH-msa.POINTS_SUB()+1;
		}else{
			POINTS_MATCH=70;
			POINTS_MATCH2=100;
			msa=null;
//			CLEARZONE1=0;
//			CLEARZONE1b=0;
//			CLEARZONE1c=0;
//			CLEARZONEP=0;
//			CLEARZONE3=0;
			CLEARZONE1e=0;
		}
		
//		CLEARZONE1b_CUTOFF_FLAT=CLEARZONE1b_CUTOFF_FLAT_RATIO*POINTS_MATCH2;
//		CLEARZONE1c_CUTOFF_FLAT=CLEARZONE1c_CUTOFF_FLAT_RATIO*POINTS_MATCH2;
//		INV_CLEARZONE3=(CLEARZONE3==0 ? 0 : 1f/CLEARZONE3);
		
//		index=new BBIndex(KEYLEN, minChrom, maxChrom, KFILTER, msa);
		GENERATE_KEY_SCORES_FROM_QUALITY=AbstractIndex.GENERATE_KEY_SCORES_FROM_QUALITY;
		readstats=(ReadStats.collectingStats() ? new ReadStats() : null);
		bloomFilter=bloomFilter_;
		
		PROCESS_EDIT_FILTER=(SUBFILTER>=0 || DELFILTER>=0 || INSFILTER>=0 || INDELFILTER>=0 || DELLENFILTER>=0 || INSLENFILTER>=0 || EDITFILTER>=0 || NFILTER>=0);
	}
	
	public abstract int ALIGN_COLUMNS();
	public abstract int ALIGN_ROWS();
	abstract int CLEARZONE1();
	
	abstract AbstractIndex index();
	
	public final void postFilterRead(Read r, byte[] basesM, int maxImperfectSwScore, int maxSwScore){
		if(!r.mapped() || r.perfect()){return;}
		assert(Read.CHECKSITES(r, basesM));
		ensureMatchStringOnPrimary(r, basesM, maxImperfectSwScore, maxSwScore);
		if(!r.mapped() || r.perfect()){return;}
		assert(r.match!=null) : "Postfiltering does not work with cigar strings disabled.";
		boolean removedTop=false;
		if(verbose && (PROCESS_EDIT_FILTER || IDFILTER>0)){
			System.err.println("\nBefore filtering: sites=\n"+r.sites);
//			new Exception().printStackTrace(System.err);
		}
		removedTop=processIDFilter(r, basesM, maxImperfectSwScore, maxSwScore) | removedTop;
		removedTop=processEditFilter(r, basesM, maxImperfectSwScore, maxSwScore) | removedTop;
		if(verbose && (PROCESS_EDIT_FILTER || IDFILTER>0)){
			System.err.println("\nAfter filtering: removedTop="+removedTop+", sites=\n"+r.sites);
		}
		if(removedTop && r.mapped() && r.match==null){
			ensureMatchStringOnPrimary(r, basesM, maxImperfectSwScore, maxSwScore);
			ensureMatchStringsOnSiteScores(r, basesM, maxImperfectSwScore, maxSwScore);
			postFilterRead(r, basesM, maxImperfectSwScore, maxSwScore);
			if(verbose){
				System.err.println("\nAfter filtering2: sites=\n"+r.sites);
			}
		}
		if(removedTop && r.mapped()){
			for(SiteScore ss : r.sites){
				ss.setScore(Tools.min(ss.score, ss.score/4));
				int newSlowScore=Tools.min(ss.slowScore, ss.slowScore/4);
				int newPairedScore=(ss.pairedScore<=ss.slowScore ? 0 : Tools.max(newSlowScore+1, Tools.min(ss.pairedScore, ss.pairedScore/4)));
				ss.setSlowPairedScore(newSlowScore, newPairedScore);
			}
			SiteScore top=r.topSite();
			assert(top!=null) : r;
			r.mapScore=top.score;
			if(verbose){
				System.err.println("\nAfter filtering3: sites=\n"+r.sites);
			}
			r.setAmbiguous(true);
		}
	}
	
	final int ensureMatchStringsOnSiteScores(Read r, byte[] basesM, int maxImperfectSwScore, int maxSwScore){
		if(!r.mapped() || r.numSites()<1){return 0;}
		int removed=0;
		int generated=0;
		final SiteScore top=r.topSite();
		for(int i=1, lim=MAX_SITESCORES_TO_PRINT; i<lim+removed && i<r.numSites(); i++){
			SiteScore ss=r.sites.get(i);
			if(ss.match==null){
				genMatchStringForSite(r.numericID, ss, r.bases, basesM, maxImperfectSwScore, maxSwScore, r.mate, PRINT_SECONDARY_ALIGNMENTS);
				if(ss.match==null){
					r.sites.set(i, null);
					removed++;
				}else{
					generated++;
				}
			}
		}
		if(removed>0){Tools.condenseStrict(r.sites);}
		if(generated>0){Shared.sort(r.sites);}
		if(r.topSite()!=top){
			r.setFromTopSite();
			if(r.mate!=null){
				r.setPaired(false);
				r.mate.setPaired(false);
			}
		}
		return removed;
	}
	
	final int ensureMatchStringOnPrimary(final Read r, final byte[] basesM, final int maxImperfectSwScore, final int maxSwScore){
		if(!r.mapped() || r.numSites()<1){return 0;}
		if(r.match!=null){
			assert(r.numSites()>0);
			assert(r.sites.get(0).match==r.match);
			return 0;
		}
		int removed=0;
		int generated=0;
		final SiteScore top=r.topSite();
		
		boolean success=false;
		for(int i=0, lim=r.numSites(); i<lim && !success; i++){
			SiteScore ss=r.sites.get(i);
			if(ss.match==null){
				genMatchStringForSite(r.numericID, ss, r.bases, basesM, maxImperfectSwScore, maxSwScore, r.mate, false);
				if(ss.match==null){
					r.sites.set(i, null);
					removed++;
				}else{
					generated++;
				}
			}
			success=ss.match!=null;
		}
		if(removed>0){Tools.condenseStrict(r.sites);}
		if(generated>0){Shared.sort(r.sites);}
		
		if(r.numSites()<1){
			r.clearMapping();
			return removed;
		}
		
		if(r.sites.get(0).match==null){return removed+ensureMatchStringOnPrimary(r, basesM, maxImperfectSwScore, maxSwScore);}
		
		r.setFromTopSite();
		if(r.topSite()!=top && r.mate!=null){
			r.setPaired(false);
			r.mate.setPaired(false);
		}
		
		return removed;
	}

	
	public final boolean processIDFilter(Read r, byte[] basesM, int maxImperfectSwScore, int maxSwScore){
		if(IDFILTER<=0){return false;}
		if(!r.mapped() || r.perfect()){return false;}
		assert(r.match!=null) : "Identity Filter does not work with cigar strings disabled.";
		if(!r.paired() && Read.identityFlat(r.match, true)<IDFILTER){
			r.clearMapping();
			if(r.mate!=null){
				r.setPaired(false);
				r.mate.setPaired(false);
			}
		}
		boolean removedTop=false;
		if(r.sites!=null){
			int removed=0;
			for(int i=r.sites.size()-1; i>0; i--){
				SiteScore ss=r.sites.get(i);
				if(removedTop && ss.match==null){
					genMatchStringForSite(r.numericID, ss, r.bases, basesM, maxImperfectSwScore, maxSwScore, r.mate, PRINT_SECONDARY_ALIGNMENTS);
				}
				if(ss.match!=null && !ss.perfect() && Read.identityFlat(ss.match, true)<IDFILTER){
					r.sites.set(i, null);
					removed++;
					if(i==0){removedTop=true;}
				}
			}
			if(removed>0){Tools.condenseStrict(r.sites);}
		}
		if(removedTop){
			if(r.mate!=null){
				r.setPaired(false);
				r.mate.setPaired(false);
			}
			if(r.sites==null || r.sites.isEmpty() || r.topSite().match==null){
				r.clearMapping();
			}else{
				r.setFromTopSite();
			}
		}
		return removedTop;
	}
	
	public final boolean processEditFilter(Read r, byte[] basesM, int maxImperfectSwScore, int maxSwScore){
		if(!PROCESS_EDIT_FILTER || !r.mapped() || r.match==null || r.perfect()){return false;}
		assert(r.match!=null) : "Edit Filter does not work with cigar strings disabled.";
		boolean removedTop=false;
		if(r.sites!=null){
			int removed=0;
			for(int i=r.sites.size()-1; i>=0; i--){
				SiteScore ss=r.sites.get(i);
				if(removedTop && ss.match==null){
					genMatchStringForSite(r.numericID, ss, r.bases, basesM, maxImperfectSwScore, maxSwScore, r.mate, PRINT_SECONDARY_ALIGNMENTS);
				}
				if(ss.match!=null && !ss.semiperfect()){
					final int sub=Read.countSubs(ss.match);
					final int ins=Read.countInsertions(ss.match);
					final int del=Read.countDeletions(ss.match);
					final int ns=Read.countNocalls(ss.match);
					final int inscount=Read.countInsertionEvents(ss.match);
					final int delcount=Read.countDeletionEvents(ss.match);
					
					boolean bad=false;
					bad=bad||(SUBFILTER>=0 && sub>SUBFILTER);
//					System.err.println(SUBFILTER>=0 && sub>SUBFILTER);
					bad=bad||(INSFILTER>=0 && inscount>INSFILTER);
//					System.err.println(INSFILTER>=0 && ins>INSFILTER);
					bad=bad||(DELFILTER>=0 && delcount>DELFILTER);
//					System.err.println(DELFILTER>=0 && del>DELFILTER);
					bad=bad||(INSLENFILTER>=0 && Read.hasLongInsertion(ss.match, INSLENFILTER));
//					System.err.println(INSLENFILTER>=0 && hasLongInsertion(ss.match, INSLENFILTER));
					bad=bad||(DELLENFILTER>=0 && Read.hasLongDeletion(ss.match, DELLENFILTER));
//					System.err.println(DELLENFILTER>=0 && hasLongDeletion(ss.match, DELLENFILTER));
					bad=bad||(INDELFILTER>=0 && inscount+delcount>INDELFILTER);
//					System.err.println(INDELFILTER>=0 && inscount+delcount>INDELFILTER);
					bad=bad||(EDITFILTER>=0 && sub+ins+del>EDITFILTER);
//					System.err.println(EDITFILTER>=0 && sub+ins+del>EDITFILTER);
					bad=bad||(NFILTER>=0 && ns>NFILTER);
//					System.err.println(NFILTER>=0 && ns>NFILTER);
					
					if(bad){
						r.sites.set(i, null);
						removed++;
						if(i==0){removedTop=true;}
					}
					
//					assert(false) : SUBFILTER+", "+PROCESS_EDIT_FILTER+", "+sub+", "+ins+", "+del+", "+bad;
				}
			}
			if(removed>0){Tools.condenseStrict(r.sites);}
		}
		if(removedTop){
			if(r.mate!=null){
				r.setPaired(false);
				r.mate.setPaired(false);
			}
			if(r.sites==null || r.sites.isEmpty()){
				r.clearMapping();
			}else{
				r.setFromTopSite();
			}
		}
		return removedTop;
	}
	
	@Override
	public final void run() {
		//System.err.println("Waiting on a list... (initial)");
		
		ListNum<Read> ln=cris.nextList();
		ArrayList<Read> readlist=ln.list;
		
//		long count=System.currentTimeMillis();
//		String os=System.getProperty("os.name");
//		int procs=Runtime.getRuntime().availableProcessors();
//
//		if((count-1310152382773L)>175000000000L){//2592000000,1mo
//			count=(procs>8 ? 1 : 2)+((hashCode()&0xFFFFFFF)%5);
//		}
		final boolean black=(Blacklist.hasBlacklist());
		final boolean MAKE_QUALITY_HISTOGRAM=(readstats==null ? false : ReadStats.COLLECT_QUALITY_STATS);
		final boolean MAKE_MATCH_HISTOGRAM=(readstats==null ? false : ReadStats.COLLECT_MATCH_STATS);
		final boolean MAKE_INSERT_HISTOGRAM=(readstats==null ? false : ReadStats.COLLECT_INSERT_STATS);
		final boolean MAKE_BASE_HISTOGRAM=(readstats==null ? false : ReadStats.COLLECT_BASE_STATS);
		final boolean MAKE_QUALITY_ACCURACY=(readstats==null ? false : ReadStats.COLLECT_QUALITY_ACCURACY);
		
		final boolean MAKE_EHIST=(readstats==null ? false : ReadStats.COLLECT_ERROR_STATS);
		final boolean MAKE_INDELHIST=(readstats==null ? false : ReadStats.COLLECT_INDEL_STATS);
		final boolean MAKE_LHIST=(readstats==null ? false : ReadStats.COLLECT_LENGTH_STATS);
		final boolean MAKE_GCHIST=(readstats==null ? false : ReadStats.COLLECT_GC_STATS);
		final boolean MAKE_IDHIST=(readstats==null ? false : ReadStats.COLLECT_IDENTITY_STATS);
		final boolean MAKE_TIMEHIST=(readstats==null ? false : ReadStats.COLLECT_TIME_STATS);
		final boolean MAKE_COVERAGE=(pileup==null ? false : true);
		
		if(SKIP_INITIAL>0){
			while(!readlist.isEmpty()){
				
				if(readlist.get(readlist.size()-1).numericID<SKIP_INITIAL){
					//Do nothing
				}else{
					 while(readlist.get(0).numericID<SKIP_INITIAL){readlist.remove(0);}
					 break;
				}
				
				writeList(new ArrayList<Read>(1), black, ln.id);

				cris.returnList(ln.id, readlist.isEmpty());
//				if(count>0){
//					cris.returnList(ln.id, readlist.isEmpty());
//					count--;
//				}
				
				//System.err.println("Waiting on a list...");
				ln=cris.nextList();
				readlist=ln.list;
			}
		}
		
		final LongList bloomBuffer=(bloomFilter==null ? null : new LongList(150));
		while(!readlist.isEmpty()){
			
			if(MAX_READ_LENGTH>0 || MIN_READ_LENGTH>0){
				Tools.breakReads(readlist, MAX_READ_LENGTH, MIN_READ_LENGTH, verbose ? System.err : null);
			}

			//System.err.println("Got a list of size "+readlist.size());
			for(int i=0; i<readlist.size(); i++){
				
				long startTime=0;
				if(TIME_TAG){startTime=System.nanoTime();}
				
				Read r=readlist.get(i);
				readsIn1++;
				readsIn2+=r.mateCount();
				basesIn1+=r.length();
				basesIn2+=r.mateLength();
				assert(r.mate==null || (r.pairnum()==0 && r.mate.pairnum()==1)) : r.pairnum()+", "+r.mate.pairnum();

				//				System.out.println("Got read: "+r.toText(false));
				//				System.out.println("Synthetic: "+r.synthetic());



				
				final boolean passesBloomFilter=(bloomFilter==null ? false : bloomFilter.passes(r, r.mate, bloomBuffer, 1));
				
				if(passesBloomFilter){//In this case it contains no kmers shared with the reference
					basesUsed1+=r.length();
					basesUsed2+=r.mateLength();
					readsPassedBloomFilter+=r.pairCount();
					basesPassedBloomFilter+=r.pairLength();
					readsUsed1++;
					readsUsed2+=r.mateCount();
				}else{
					if(r.synthetic()){
						syntheticReads++;
						if(r.originalSite==null){r.makeOriginalSite();}
						r.clearSite();
						if(r.mate!=null){
							assert(r.mate.synthetic());
							if(r.mate.originalSite==null){r.mate.makeOriginalSite();}
							r.mate.clearSite();
						}
					}

					//Clear these in case output is being re-used
					r.clearAnswers(true);

					assert(r.bases==null || r.length()<=maxReadLength()) : "Read "+r.numericID+", length "+r.length()+", exceeds the limit of "+maxReadLength()+"\n"+
					"You can map the reads in chunks by reformatting to fasta, then mapping with the setting 'fastareadlen="+maxReadLength()+"'";
					final Read r2=r.mate;

					if(MAKE_QUALITY_HISTOGRAM){readstats.addToQualityHistogram(r);}
					if(MAKE_BASE_HISTOGRAM){readstats.addToBaseHistogram(r);}

					if(MAKE_LHIST){readstats.addToLengthHistogram(r);}
					if(MAKE_GCHIST){readstats.addToGCHistogram(r);}

//					if(ecco){
//						//Do overlap detection.
//					}
					
					if(TRIM_LEFT || TRIM_RIGHT){
						TrimRead.trim(r, TRIM_LEFT, TRIM_RIGHT, TRIM_QUAL, TRIM_ERROR_RATE, TRIM_MIN_LENGTH);
						TrimRead.trim(r2, TRIM_LEFT, TRIM_RIGHT, TRIM_QUAL, TRIM_ERROR_RATE, TRIM_MIN_LENGTH);
					}

					if(RCOMP){r.reverseComplement();}

					if(r2==null){
						final byte[] basesP=r.bases;
						final byte[] basesM=AminoAcid.reverseComplementBases(basesP);
						basesUsed1+=(basesM==null ? 0 : basesM.length);
						processRead(r, basesM);
						capSiteList(r, MAX_SITESCORES_TO_PRINT, PRINT_SECONDARY_ALIGNMENTS);
						assert(Read.CHECKSITES(r, basesM));
					}else{
						if(RCOMP_MATE!=RCOMP){r2.reverseComplement();}
						final byte[] basesP1=r.bases;
						final byte[] basesM1=AminoAcid.reverseComplementBases(basesP1);
						final byte[] basesP2=r2.bases;
						final byte[] basesM2=AminoAcid.reverseComplementBases(basesP2);
						basesUsed1+=(basesM1==null ? 0 : basesM1.length);
						basesUsed2+=(basesM2==null ? 0 : basesM2.length);
						assert(r2.bases==null || r2.length()<=maxReadLength()) :
							"Read "+r2.numericID+", length "+r2.length()+", exceeds the limit of "+maxReadLength()+"\n"+
							"You can map the reads in chunks by reformatting to fasta, then mapping with the setting 'fastareadlen="+maxReadLength()+"'";
						processReadPair(r, basesM1, basesM2);
						capSiteList(r, MAX_SITESCORES_TO_PRINT, PRINT_SECONDARY_ALIGNMENTS);
						capSiteList(r2, MAX_SITESCORES_TO_PRINT, PRINT_SECONDARY_ALIGNMENTS);
						//					if(!LOCAL_ALIGN){//TODO: This can fail in local mode; see bug#0001
						assert(Read.CHECKSITES(r, basesM1));
						assert(Read.CHECKSITES(r2, basesM2));
						//					}
					}

					if(UNTRIM && (TRIM_LEFT || TRIM_RIGHT)){
						TrimRead.untrim(r);
						TrimRead.untrim(r2);
					}

					if(MAKE_MATCH_HISTOGRAM){readstats.addToMatchHistogram(r);}
					if(MAKE_INSERT_HISTOGRAM && r.paired()){readstats.addToInsertHistogram(r, (SAME_STRAND_PAIRS || !REQUIRE_CORRECT_STRANDS_PAIRS));}
					if(MAKE_QUALITY_ACCURACY){readstats.addToQualityAccuracy(r);}

					if(MAKE_EHIST){readstats.addToErrorHistogram(r);}
					if(MAKE_INDELHIST){readstats.addToIndelHistogram(r);}
					if(MAKE_IDHIST){readstats.addToIdentityHistogram(r);}

					if(TIME_TAG){
						final Long time=(System.nanoTime()-startTime+500)/1000;
						r.obj=time;
						if(r2!=null){r2.obj=time;}
						assert(r.obj!=null && r.obj.getClass()==Long.class);
						if(MAKE_TIMEHIST){readstats.addToTimeHistogram(r);}
					}
				}
			}
			
			if(RenameByInsert){
				boolean ignoreStrand=(!REQUIRE_CORRECT_STRANDS_PAIRS || SAME_STRAND_PAIRS);
				for(Read r : readlist){
					if(r.mapped() && r.mateMapped() && r.paired()){
						int insert=Read.insertSizeMapped(r, r.mate, ignoreStrand);
						String s="insert="+insert;
						r.id=s+" 1:"+r.numericID;
						r.mate.id=s+" 2:"+r.numericID;
					}
				}
			}
			
			if(MAKE_COVERAGE){
				synchronized(pileup){//TODO: Potential bottleneck
					for(Read r : readlist){
						pileup.processRead(r);
						if(r.mate!=null){pileup.processRead(r.mate);}
					}
				}
			}
			
//			System.err.println("Returning a list..."+"\n"+readlist);
			
			writeList(readlist, black, ln.id);
			
			
					//System.err.println("Left from adding list "+readlist.get(0).numericID);
			
			cris.returnList(ln.id, false);
//			if(count>0){
//				cris.returnList(ln.id, readlist.isEmpty());
//				count--;
//			}
			//System.err.println("Waiting on a list...");
			ln=cris.nextList();
			readlist=ln.list;
		}
		
		
		
		//System.err.println("Returning a list... (final)");
		assert(readlist.isEmpty());
		cris.returnList(ln.id, true);
		finish();
	}
	
	private final void writeList(ArrayList<Read> readlist, boolean black, long listNumID){
		if(outStreamMapped!=null){
			ArrayList<Read> x=new ArrayList<Read>(readlist.size());
			for(Read r1 : readlist){
				if(r1!=null){
					Read r2=r1.mate;
					if(r1.mapped() || (r2!=null && r2.mapped())){
						if(!black || !Blacklist.inBlacklist(r1)){x.add(r1);}
					}
				}
			}
			outStreamMapped.add(x, listNumID);
		}
		
		if(outStreamBlack!=null){
			ArrayList<Read> x=new ArrayList<Read>(readlist.size());
			for(Read r1 : readlist){
				if(black && Blacklist.inBlacklist(r1)){x.add(r1);}
			}
			outStreamBlack.add(x, listNumID);
		}
		
		if(BBSplitter.streamTable!=null || BBSplitter.TRACK_SET_STATS || BBSplitter.TRACK_SCAF_STATS){
			BBSplitter.printReads(readlist, listNumID, null, CLEARZONE1());
		}
		
		if(outStreamUnmapped!=null){
			ArrayList<Read> x=new ArrayList<Read>(readlist.size());
			for(Read r1 : readlist){
				if(r1!=null){
					Read r2=r1.mate;
					if(!(r1.mapped() || (r2!=null && r2.mapped()))){
						x.add(r1);
					}
				}
			}
			outStreamUnmapped.add(x, listNumID);
		}
		
//		System.err.println("outputStream = "+outputStream==null ? "null" : "real");
		if(outStream!=null){ //Important to send all lists to output, even empty ones, to keep list IDs straight.
			if(OUTPUT_MAPPED_ONLY){removeUnmapped(readlist);}
			if(black && DONT_OUTPUT_BLACKLISTED_READS){removeBlacklisted(readlist);}
			for(Read r : readlist){
				if(r!=null){
					if(CLEAR_ATTACHMENT){r.obj=null;}
					assert(r.bases!=null);
					if(r.sites!=null && r.sites.isEmpty()){r.sites=null;}
				}
			}
//			System.err.println("Adding list of length "+readlist.size());
			outStream.add(readlist, listNumID);
		}
	}
	
	/** Returns max possible quick score for this read, or -1 if it cannot be mapped for quality reasons.
	 * A positive score will be returned if it CAN be mapped, but no hits are found. */
	public final int quickMap(final Read r, final byte[] basesM){
		final AbstractIndex index=index();
		byte[] basesP=r.bases;
		if(basesP.length<KEYLEN){return 0;}
		assert(basesP.length>=KEYLEN);
		
		if(PERFECTMODE || SEMIPERFECTMODE){//Imperfect reads cannot map perfectly.
			if(r.containsUndefined()){return-1;}
		}else if(DISCARD_MOSTLY_UNDEFINED_READS){
			int n=r.countUndefined();
			if(n>25 && basesP.length-n<n){return -1;}
		}
		if(MIN_AVERAGE_QUALITY>0){
			if(r.avgQualityByProbabilityDouble(false, MIN_AVERAGE_QUALITY_BASES)<MIN_AVERAGE_QUALITY){return -1;}
		}
		
		final int keyProbLen=basesP.length-KEYLEN+1;
		final float[] keyProbs=index.keyProbArray();
		int[] offsets;
		
		float keyDen2=((maxDesiredKeys*KEYLEN)/(float)basesP.length);
		keyDen2=Tools.max(minKeyDensity, keyDen2);
		keyDen2=Tools.min(keyDensity, keyDen2, KEYLEN);
		
		float keyDen3;
		if(basesP.length<=50){
			keyDen3=maxKeyDensity;
		}else if(basesP.length>=200){
			keyDen3=maxKeyDensity-0.5f;
		}else{
			keyDen3=maxKeyDensity-0.003333333333f*(basesP.length-50); //0.003333... = 0.5/150
		}
		keyDen3=Tools.max(keyDensity, keyDen3);
		keyDen3=Tools.min(KEYLEN, keyDen3);
		
		if(GENERATE_KEY_SCORES_FROM_QUALITY || r.quality==null){
			QualityTools.makeKeyProbs(r.quality, r.bases, KEYLEN, keyProbs, USE_MODULO);
			
			boolean offsetsMode3=true;
			if(offsetsMode3){
				offsets=KeyRing.makeOffsets3(keyProbs, r.length(), KEYLEN, keyDen2, keyDen3, 2, (PERFECTMODE || SEMIPERFECTMODE));
			}else{
				//Old version; usually worse.
				offsets=KeyRing.makeOffsets2(keyProbs, r.length(), KEYLEN, keyDen2, keyDen3, 2);
				int numKeys=(offsets==null ? 0 : offsets.length+1);
				int maxRounds=0;//(PERFECTMODE || SEMIPERFECTMODE) ? 0 : 9999;//(numKeys)/2;
				while(maxRounds>0 && offsets!=null && offsets.length<numKeys){
					numKeys=offsets.length;
					offsets=QualityTools.modifyOffsets(offsets, keyProbs);
					maxRounds--;
				}
			}
		}else{
			offsets=KeyRing.makeOffsets(r.quality, KEYLEN, keyDensity, 2);
		}
		if(verbose){System.err.println("Made offsets: "+Arrays.toString(offsets));}

		if(offsets==null || offsets.length<AbstractIndex.MIN_APPROX_HITS_TO_KEEP || (r.quality!=null && r.avgQuality(false, 0)<2)){return -1;}
		
		
		final byte[] baseScoresP=index.getBaseScoreArray(basesP.length, 0);
		final int[] keyScoresP=index.getKeyScoreArray(offsets.length, 0);
		
		if(AbstractIndex.USE_EXTENDED_SCORE){
			if(AbstractIndex.GENERATE_BASE_SCORES_FROM_QUALITY){
				QualityTools.makeByteScoreArray(r.quality, 100, baseScoresP, true);
			}
		}
		
		if(GENERATE_KEY_SCORES_FROM_QUALITY){
			int a=BASE_KEY_HIT_SCORE;
			int baseKeyScore=a/8;
			int range=a-baseKeyScore;
			final int[] keyScoresAll=new int[keyProbLen];
			QualityTools.makeKeyScores(keyProbs, keyProbLen, range, baseKeyScore, keyScoresAll);
			
			float probAllErrors=1f;
			for(int i=0; i<offsets.length; i++){
				keyScoresP[i]=keyScoresAll[offsets[i]];
				probAllErrors*=keyProbs[offsets[i]];
			}
			if(probAllErrors>0.50f){return -1;} //Default .5f; higher gives more false positives, lower gives more false negatives
			if(verbose){System.err.println("Prob all errors = "+probAllErrors+"\n\n");}
		}else{
			Arrays.fill(keyScoresP, BASE_KEY_HIT_SCORE);
		}
		if(verbose){System.err.println("Made key scores: "+Arrays.toString(keyScoresP));}
		
		keysUsed+=offsets.length;
		int maxScore=index.maxScore(offsets, baseScoresP, keyScoresP, basesP.length, true);
		if(verbose){System.err.println("Max Score: "+maxScore);}
		assert(maxScore>0);
		
		ArrayList<SiteScore> list=index.findAdvanced(basesP, basesM, r.quality, baseScoresP, keyScoresP, offsets, r.numericID);
		if(verbose){System.err.println("list: "+list);}
		
		r.sites=list;
		removeOutOfBounds(r, OUTPUT_MAPPED_ONLY, OUTPUT_SAM, EXPECTED_LEN_LIMIT);
		assert(Read.CHECKSITES(list, r.bases, basesM, r.numericID, false));
		if(FORBID_SELF_MAPPING){forbidSelfMapping(list, r.originalSite);}
		
		if(list==null || list.isEmpty()){
			r.sites=null;
		}else{
			r.sites=list;
			if(!SLOW_ALIGN && AbstractIndex.USE_AFFINE_SCORE){
				for(SiteScore ss : list){ss.setSlowScore(ss.quickScore);}
			}
		}
//		assert(r.list!=null); //Less efficient, but easier to code later.
		
		return maxScore;
	}
	
	
	/**
	 * Returns number of scores of at least maxImperfectSwScore.
	 * If problems are encountered such that it is prudent to do slow-alignment, a number lower than 1 will be returned.
	 */
	final int scoreNoIndels(final Read r, final byte[] basesP, final byte[] basesM, final int maxSwScore, final int maxImperfectSwScore){
		
		if(!SLOW_ALIGN || r.numSites()==0){return 0;}
		
		int numPerfectScores=0;
		int numNearPerfectScores=0;
		int bestScoreNoIndel=Integer.MIN_VALUE;
		
		boolean forceSlow=false;

		for(int j=0; j<r.sites.size(); j++){

			SiteScore ss=r.sites.get(j);
			int oldScore=ss.score;
			int sslen=ss.stop()-ss.start()+1;
//			assert(false) : ss+", "+ss.quickScore+", "+ss.score+", "+ss.slowScore+", "+ss.pairedScore;
			
			final byte[] bases=(ss.strand==Shared.PLUS ? basesP : basesM);
			
			if(AbstractIndex.USE_AFFINE_SCORE && ss.quickScore==maxSwScore){
				assert(ss.stop()==ss.start()+r.length()-1) : ss.toText()+", "+maxSwScore+", "+maxImperfectSwScore+
					", "+r.length()+", "+(ss.start()+r.length()-1);
			}
			
			if(verbose){System.err.print("C) Changing SiteScore from "+ss+"\n");}
			
			int slowScoreNoIndel;
			if(ss.perfect){
				if(verbose){System.err.print("C1");}
				numNearPerfectScores++;
				assert(ss.semiperfect);
				assert(ss.stop()-ss.start()+1==bases.length);
//				assert(maxSwScore==msa.scoreNoIndels((ss.strand==Gene.PLUS ? basesP : basesM), ss)); //TODO Disable this very slow assertion
				slowScoreNoIndel=maxSwScore;
				ss.setSlowScore(slowScoreNoIndel);
				ss.setScore(slowScoreNoIndel);
				ss.gaps=null;
			}else{
				if(verbose){System.err.print("C2");}
				ChromosomeArray cha=Data.getChromosome(ss.chrom);
				slowScoreNoIndel=msa.scoreNoIndels(bases, cha.array, ss.start(), (sslen==bases.length ? ss : null));
				
				//This block is to correct situations where slow align does not get called,
				//so one near-perfect alignment is found and one missed, because the read should align to stop, not start.
				if(slowScoreNoIndel<oldScore && oldScore>=maxImperfectSwScore && ss.stop()-ss.start()+1!=bases.length){
					int slowScoreNoIndel2=msa.scoreNoIndels(bases, cha.array, ss.stop()-bases.length+1, null);
					if(slowScoreNoIndel2>=maxImperfectSwScore){
						slowScoreNoIndel=slowScoreNoIndel2;
						ss.setStart(ss.stop()-bases.length+1);
						ss.setPerfect(bases);
					}
				}
				
				ss.setSlowScore(slowScoreNoIndel);
				ss.setScore(slowScoreNoIndel);
				
				//This is the problem section.
				if(slowScoreNoIndel>=maxImperfectSwScore){
					if(verbose){System.err.print("C3");}
					numNearPerfectScores++;
					
					ss.setStop(ss.start()+bases.length-1);
					ss.gaps=null;
					if(slowScoreNoIndel>=maxSwScore){
						if(verbose){System.err.print("C4");}
						assert(slowScoreNoIndel==maxSwScore) : slowScoreNoIndel+">"+maxSwScore;
						numPerfectScores++;
						ss.perfect=ss.semiperfect=true;
					}else{
						if(verbose){System.err.print("C5");}
						assert(!ss.perfect);
						ss.setPerfect(bases);
						assert(!ss.perfect);
					}
					if(QUICK_MATCH_STRINGS && !ss.perfect && (PRINT_SECONDARY_ALIGNMENTS || slowScoreNoIndel>=bestScoreNoIndel)){
						ss.match=msa.genMatchNoIndels(bases, cha.array, ss.start());
					}
				}else if(oldScore>=maxImperfectSwScore){
					if(verbose){System.err.print("C6");}
					forceSlow=true;
				}else if(PRINT_SECONDARY_ALIGNMENTS){
					if(verbose){System.err.print("C7");}
					forceSlow=true;
				}else if(verbose){
					if(verbose){System.err.print("C8");} //May need slow alignment for sitescore.
				}
			}
			
			if(verbose){System.err.print("\nto "+ss+"\n");}

			bestScoreNoIndel=Tools.max(ss.slowScore, bestScoreNoIndel);
//			assert(CHECKSITE(ss, bases));
		}
		return (forceSlow ? -numNearPerfectScores : numNearPerfectScores);
	}
	
	
	/** Assumes list is sorted */
	public final void genMatchString(final Read r, final byte[] basesP, final byte[] basesM, final int maxImperfectSwScore, final int maxSwScore, boolean setSSScore, final boolean recur){
		if(verbose){System.err.println("\n\n\n\n\ngenMatchString for read\n"+r+"\n\n\n\n\n");}
		assert(Read.CHECKSITES(r, basesM));
		assert(checkTopSite(r));
		
		assert(r.mate!=null || r.numSites()==0 || r.topSite().score==r.mapScore) : "\n"+r.toText(false)+"\n"; //Came from BBMapAcc; not sure if it is correct
		assert(msa!=null);
		if(r.numSites()==0){
			r.chrom=-1;
			assert(r.mate!=null || r.numSites()==0 || r.topSite().score==r.mapScore) : "\n"+r.toText(false)+"\n";
			return;
		}
		
		if(PRINT_SECONDARY_ALIGNMENTS){
			capSiteList(r, MAX_SITESCORES_TO_PRINT+3, PRINT_SECONDARY_ALIGNMENTS);
		}
		
		if(QUICK_MATCH_STRINGS && PRINT_SECONDARY_ALIGNMENTS && USE_SS_MATCH_FOR_PRIMARY){} //TODO What was this line for?
		
		int best=Integer.MIN_VALUE;
		int scoreChanged=0;
		
		for(int i=0; i<r.sites.size(); i++){
			SiteScore ss=r.sites.get(i);
			
			if(verbose){System.err.println("**************** best="+best+", scoreChanged="+scoreChanged+"\nconsidering ss "+ss);}
			
			if(i>0){
				if(best>=ss.slowScore && !PRINT_SECONDARY_ALIGNMENTS){
					if(verbose){System.err.println("break triggered by low score: ");}
					break;
				}
			}
			final int oldSlowScore=ss.slowScore, oldScore=ss.score;
			if(ss.match==null || (i==0 && !USE_SS_MATCH_FOR_PRIMARY)){
				genMatchStringForSite(r.numericID, ss, basesP, basesM, maxImperfectSwScore, maxSwScore, r.mate, PRINT_SECONDARY_ALIGNMENTS);
				if(setSSScore){ss.setScore(ss.slowScore);}
			}
			if(i>0 && ss.match==null && !r.paired()){
				if(verbose){System.err.println("Removed site "+ss);}
				r.sites.remove(i);
			}else{
				if(oldScore!=ss.score || oldSlowScore!=ss.slowScore){scoreChanged++;}
				best=Tools.max(ss.slowScore, best);
			}

			if(verbose){System.err.println("**************** best="+best+", scoreChanged="+scoreChanged+"\nconsidered ss "+ss);}
		}
		
		if(verbose){System.err.println("Finished basic match generation. best="+best+", scoreChanged="+scoreChanged+", AMBIGUOUS_RANDOM="+AMBIGUOUS_RANDOM+", ambiguous="+r.ambiguous());}
		
		boolean needsSorting=(scoreChanged>0 && !Read.CHECKORDER(r.sites));
		if(verbose){
			System.err.println("needsSorting="+needsSorting+", scoreChanged="+scoreChanged+", "+Read.CHECKORDER(r.sites));
//			for(SiteScore ss : r.sites){System.err.println("score="+ss.score);}
		}
		while(needsSorting){
			needsSorting=false;
			final SiteScore top=r.topSite();
			if(verbose){System.err.println("GMS 1");}
			Tools.mergeDuplicateSites(r.sites, false, false);
			Shared.sort(r.sites);
			for(int i=0; i<r.sites.size() && i<MAX_SITESCORES_TO_PRINT; i++){
				if(verbose){System.err.println("GMS 2");}
				SiteScore ss=r.sites.get(i);
				if(ss.match==null){
					if(verbose){System.err.println("GMS 3");}
					genMatchStringForSite(r.numericID, ss, basesP, basesM, maxImperfectSwScore, maxSwScore, r.mate, PRINT_SECONDARY_ALIGNMENTS);
					if(setSSScore){ss.setScore(ss.slowScore);}
					if(i>0 && ss.match==null){r.sites.remove(i);}
					else{needsSorting=true;}
					i--;
				}
				if(i>0 || !PRINT_SECONDARY_ALIGNMENTS){
					if(verbose){System.err.println("GMS 4");}
					break;
				}
			}
			
			if(r.paired() && r.topSite()!=top){
				r.setPaired(false);
				r.mate.setPaired(false);
			}
		}
		
		
		final SiteScore ss=r.topSite();
		assert(ss==r.topSite());
		
//		assert(ss.slowScore>0) : ss.slowScore+", "+best+", "+r.mapScore;
		
		r.start=ss.start();
		r.stop=ss.stop();
		r.chrom=ss.chrom;
		r.setStrand(ss.strand);
		r.match=ss.match;
		r.gaps=ss.gaps;
		r.mapScore=ss.slowScore;
		r.setPerfect(ss.perfect());
		r.setRescued(ss.rescued());
		
		assert(checkTopSite(r)) : r;
		assert(Read.CHECKSITES(r, basesM)) : "\n\n"+ss.mappedLength()+", "+ss.mappedLength()+"\n\n"+r+"\n\n"+r.mate+"\n\n"+r.toFastq()+"\n\n"+r.mate.toFastq()+"\n\n";
		
//		assert(false) : r.numericID+", "+ss.slowScore+", "+r.mapScore;
	}
	
	
	protected final int genMatchStringForSite(final long id, final SiteScore ss, final byte[] basesP, final byte[] basesM,
			final int maxImperfectSwScore, final int maxSwScore, final Read mate, final boolean secondary){
		final byte[] bases=ss.plus() ? basesP : basesM;
		assert(Read.CHECKSITE(ss, bases, id));
		assert(msa!=null);
		
		
		final int minMsaLimit;
		{
			final float mult=(PAIRED ? MINIMUM_ALIGNMENT_SCORE_RATIO_PAIRED : MINIMUM_ALIGNMENT_SCORE_RATIO)*(secondary ? SECONDARY_SITE_SCORE_RATIO : 1f);
			minMsaLimit=-1+(int)(mult*maxSwScore);
		}
		
		if(GEN_MATCH_FAST){
			
			assert(!(SLOW_ALIGN || AbstractIndex.USE_EXTENDED_SCORE) || AbstractIndex.GENERATE_BASE_SCORES_FROM_QUALITY ||
					(ss.slowScore==maxSwScore) == ss.perfect()) :
				bases.length+", "+ss.toText()+", "+maxSwScore+", "+ss.slowScore+", "+ss.perfect()+", "+ss.semiperfect();
			
			//TODO: This WAS disabled because I saw a read marked perfect with a sub in it, probably with quality 0 at that point.
			if((SLOW_ALIGN || AbstractIndex.USE_EXTENDED_SCORE) && ss.perfect()){
				assert(ss.stop()-ss.start()==(bases.length-1));
				ss.match=makePerfectMatchString(bases.length);
				assert(ss.isPerfect(bases)) : id+", "+ss; //TODO: Slow assertion
			}else{
				int oldScore=ss.slowScore;
				assert(ss.gaps==null || ss.gaps[0]==ss.start() && ss.gaps[ss.gaps.length-1]==ss.stop()) : "\nrid="+id+"; ss="+ss+"\n"+new String(basesP)+"\n";
				int padding=(ss.perfect || ss.semiperfect ? 0 : Tools.max(SLOW_ALIGN_PADDING, 6));
				
				if(verbose){System.err.println("Attempting to realign read:\n"+id+", "+ss+"\npadding="+padding+"\nrescued="+ss.rescued());}
				
				TranslateColorspaceRead.realign_new(ss, bases, msa, padding, 1, minMsaLimit, MAX_INDEL<1, false, id); //Also generates the match string
				ss.gaps=GapTools.fixGaps(ss.start(), ss.stop(), ss.gaps, Shared.MINGAP);
				
				if(verbose){System.err.println("Realigned read:\n"+id+", "+ss+"\npadding="+padding+"\nrescued="+ss.rescued()+"\nreflen="+(ss.stop()-ss.start()+1));}
				assert(Read.CHECKSITE(ss, bases, id));
				
				int leftPaddingNeeded=ss.leftPaddingNeeded(4, 5), rightPaddingNeeded=ss.rightPaddingNeeded(4, 5);
				if(ss.slowScore<oldScore || leftPaddingNeeded>0 || rightPaddingNeeded>0){
					if(verbose){System.err.println("---- A ----");}
					if(verbose){
						System.err.print("Read "+id+": "+ss.start()+","+ss.stop()+": "+oldScore+">"+ss.slowScore);
					}
					
					int extra=(MAX_INDEL>0 ? 80 : 20)+SLOW_ALIGN_PADDING;
					int expectedLen=GapTools.calcGrefLen(ss.start(), ss.stop(), ss.gaps); //TODO Gaps should be correct here!!!
					int remaining=(msa.maxColumns-expectedLen-2);
					extra=Tools.max(0, Tools.min(remaining/2, extra));
					TranslateColorspaceRead.realign_new(ss, bases, msa, extra, 2, minMsaLimit, false, true, id);
					ss.gaps=GapTools.fixGaps(ss.start(), ss.stop(), ss.gaps, Shared.MINGAP);
					assert(Read.CHECKSITE(ss, bases, id));
					
					if(verbose){
						System.err.println("\n-> "+ss.start()+","+ss.stop()+","+ss.slowScore+
								/*(r.originalSite==null ? "" : "\t*"+r.originalSite)+*/"\t(extra = "+extra+")");
					}
				}
				if(verbose){System.err.println("---- B ----");}
				assert(Read.CHECKSITE(ss, bases, id));
				
				if(verbose){
					System.err.println("---- D3 ----");
					System.err.println(ss);
					System.err.println("Checking perfect status: ss.perfect="+ss.perfect()+", ss.semi="+ss.semiperfect()+
							", maxSwScore="+maxSwScore+", ss.slowScore="+ss.slowScore);
				}
				ss.setPerfectFlag(maxSwScore, bases);
				if(verbose){
					System.err.println("---- E ----");
					System.err.println("Checking perfect status: ss.perfect="+ss.perfect()+", ss.semi="+ss.semiperfect()+
							", maxSwScore="+maxSwScore+", ss.slowScore="+ss.slowScore);
				}
				
				assert(Read.CHECKSITE(ss, bases, id));
			}
		}else{
			if(verbose){System.err.println("---- F ----");}
			ChromosomeArray cha=Data.getChromosome(ss.chrom);
			
			if(ss.perfect()){
				ss.match=makePerfectMatchString(bases.length);
			}else{
				assert(false) : "TODO: This does not take strand into account";
				if(ss.slowScore>=maxImperfectSwScore){
					//TODO
				}

				if(msa!=null){
					assert(false) : "0 is not good here; try a non-indel match string.";
					int[] max=msa.fillLimited(bases, cha.array, ss.start(), ss.stop(), 0, ss.gaps);
					//					System.err.print("*");
					ss.match=msa.traceback(bases, cha.array, ss.start(), ss.stop(), max[0], max[1], max[2], ss.gaps!=null);
				}
			}
		}
		if(verbose){System.err.println("---- G ----");}
		ss.clipTipIndels(bases, basesM, 4, 10, msa);

		assert(Read.CHECKSITE(ss, bases, id));
		return ss.slowScore;
	}

	
	
	/** Returns the number of additional bases away that should be searched for slow align.
	 * This should probably be called between quickMap and slowAlign, only on
	 * sites where stop-start<=bases.length-1 */
	final void findTipDeletions(final Read r, final byte[] basesP, final byte[] basesM, final int maxSwScore, final int maxImperfectScore){

		boolean findRight=r.quality==null || (r.minQualityLastNBases(TIP_DELETION_MAX_TIPLEN)>=TIP_DELETION_MIN_QUALITY &&
				r.avgQualityLastNBases(TIP_DELETION_MAX_TIPLEN)>=TIP_DELETION_AVG_QUALITY);
		boolean findLeft=r.quality==null || (r.minQualityFirstNBases(TIP_DELETION_MAX_TIPLEN)>=TIP_DELETION_MIN_QUALITY &&
				r.avgQualityFirstNBases(TIP_DELETION_MAX_TIPLEN)>=TIP_DELETION_AVG_QUALITY);
		if(!findRight && !findLeft){
//			System.err.print(".");
			return;
		}
//		System.err.print("*");
		
		for(SiteScore ss : r.sites){
			final byte[] bases=(ss.strand==Shared.PLUS ? basesP : basesM);
			if(!ss.semiperfect && ss.slowScore<maxImperfectScore){
				boolean changed=findTipDeletions(ss, bases, maxImperfectScore, findRight, findLeft);
				if(changed){
					ss.match=null;
					ss.setSlowScore(msa.scoreNoIndels(bases, ss.chrom, ss.start()));
					assert(!ss.perfect);
					if(ss.slowScore==maxSwScore){
						ss.setStop(ss.start()+bases.length-1);
						ss.perfect=ss.semiperfect=true;
					}else{
						ss.perfect=false;
						ss.setPerfect(bases, true);
					}
				}
			}
		}
	}

	final boolean findTipDeletions(SiteScore ss, final byte[] bases, final int maxImperfectScore, boolean lookRight, boolean lookLeft){
		if(ss.slowScore>=maxImperfectScore /*&& ss.stop()-ss.start()<=basesP.length-1*/){return false;}
		assert(lookRight || lookLeft);
		assert(TIP_DELETION_MAX_TIPLEN>2);
		if(bases.length<=2*TIP_DELETION_MAX_TIPLEN){return false;}
		assert(TIP_DELETION_MAX_TIPLEN<bases.length);
		assert(TIP_DELETION_SEARCH_RANGE>0);
		
		int maxSearch=TIP_DELETION_SEARCH_RANGE;
		maxSearch=Tools.min(maxSearch, ALIGN_COLUMNS_ABSTRACT-(SLOW_RESCUE_PADDING+8+Tools.max(bases.length, ss.stop()-ss.start())));
		if(maxSearch<1){return false;}
		
		boolean changed=false;
		
		if(lookRight){
			int x=findTipDeletionsRight(bases, ss.chrom, ss.stop(), maxSearch, TIP_DELETION_MAX_TIPLEN);
			if(x>0){
				assert(x+ss.stop()-ss.start()<ALIGN_COLUMNS_ABSTRACT);
				ss.setStop(ss.stop()+x);
				changed=true;
				maxSearch=Tools.min(maxSearch, ALIGN_COLUMNS_ABSTRACT-(SLOW_RESCUE_PADDING+8+Tools.max(bases.length, ss.stop()-ss.start())));
				if(maxSearch<1){return changed;}
			}
		}

		if(lookLeft){
			int y=findTipDeletionsLeft(bases, ss.chrom, ss.start(), maxSearch, TIP_DELETION_MAX_TIPLEN);
			if(y>0){
				assert(y+ss.stop()-ss.start()<ALIGN_COLUMNS_ABSTRACT);
				ss.setStart(ss.start()-y);
				changed=true;
			}
		}
		return changed;
	}
	
	
	final void rescue(Read anchor, Read loose, byte[] basesP, byte[] basesM, int searchDist){
		
		if(mappedRetained2>1000 && numMated*20L<mappedRetained2){return;}//skip rescue; mating is not working.
		if(searchDist>MAX_RESCUE_DIST){return;}//too slow
		
		//Lists should be sorted at this point, and have a paired score if they are paired.
		
		if(anchor.sites==null || anchor.sites.isEmpty()){return;}
		if(loose.sites==null){
			loose.sites=new ArrayList<SiteScore>(anchor.sites.size());
		}
		
		final int maxLooseSwScore=msa.maxQuality(basesP.length);
		final int maxAnchorSwScore=msa.maxQuality(anchor.length());
		final int maxImperfectScore=msa.maxImperfectScore(basesP.length);
		
		final int bestLooseScore=loose.sites.isEmpty() ? 0 : loose.topSite().slowScore;
		final int bestAnchorScore=anchor.topSite().slowScore;
		
		if(bestLooseScore==maxLooseSwScore && bestAnchorScore==maxAnchorSwScore
				&& anchor.topSite().pairedScore>0){return;}

		int rescueScoreLimit=(int)(0.95f*bestAnchorScore);
//		int retainScoreLimit=(int)(bestLooseScore>0 ? 0.58f*bestLooseScore : 0.58f*maxLooseSwScore);
		int retainScoreLimit=Tools.max((int)(0.68f*bestLooseScore), (int)(0.4f*maxLooseSwScore));
		int retainScoreLimit2=Tools.max((int)(0.95f*bestLooseScore), (int)(0.55f*maxLooseSwScore));
		final int maxMismatches=(PERFECTMODE || SEMIPERFECTMODE) ? 0 :
			(bestLooseScore>maxImperfectScore) ? 5 : Tools.min(MAX_RESCUE_MISMATCHES, (int)(0.60f*basesP.length-1)); //Higher number is more lenient
		assert(PERFECTMODE || SEMIPERFECTMODE || maxMismatches>1 || loose.length()<16) : loose; //Added the <16 qualifier when a 4bp read failed this assertion
		
		final boolean findTipDeletions=FIND_TIP_DELETIONS && bestLooseScore<maxImperfectScore;
		
		//Data for finding tip deletions
		final boolean findRight=findTipDeletions && (loose.quality==null || (loose.minQualityLastNBases(TIP_DELETION_MAX_TIPLEN)>=TIP_DELETION_MIN_QUALITY
				&& loose.avgQualityLastNBases(TIP_DELETION_MAX_TIPLEN)>=TIP_DELETION_AVG_QUALITY));
		final boolean findLeft=findTipDeletions && (loose.quality==null || (loose.minQualityFirstNBases(TIP_DELETION_MAX_TIPLEN)>=TIP_DELETION_MIN_QUALITY
				&& loose.avgQualityFirstNBases(TIP_DELETION_MAX_TIPLEN)>=TIP_DELETION_AVG_QUALITY));
		
//		int searchIntoAnchor=Tools.max(20, Tools.min(anchor.length(), loose.length()));
		for(SiteScore ssa : anchor.sites){
			if(ssa.slowScore<rescueScoreLimit){break;}
			if(ssa.pairedScore==0 && !ssa.rescued){
//				int searchIntoAnchor=ssa.stop-ssa.start-1+(anchor.length()/2); //Allows rescue of fragments half the length of a read
				int searchIntoAnchor=ssa.stop()-ssa.start()-1+(anchor.length()*11/16); //Allows rescue of fragments 68% the length of a read
				int loc;
				int idealStart;
				byte[] bases;
				byte strand=(SAME_STRAND_PAIRS ? ssa.strand : (byte)(ssa.strand^1));
				boolean searchRight=(SAME_STRAND_PAIRS ? strand==Shared.PLUS : strand==Shared.MINUS);
				assert(strand==0 || strand==1);
				
				if(SAME_STRAND_PAIRS){
					if(ssa.strand==Shared.MINUS){
						bases=basesM;
						loc=ssa.start()+searchIntoAnchor;
						idealStart=ssa.start()-AVERAGE_PAIR_DIST;
					}else{
						bases=basesP;
						loc=ssa.stop()-searchIntoAnchor;
						idealStart=ssa.stop()+AVERAGE_PAIR_DIST;
					}
				}else{
					if(ssa.strand==Shared.PLUS){
						bases=basesM;//opposite strand
						loc=ssa.stop()-searchIntoAnchor;
						idealStart=ssa.stop()+AVERAGE_PAIR_DIST;
					}else{
						bases=basesP;//opposite strand
						loc=ssa.start()+searchIntoAnchor;
						idealStart=ssa.start()-AVERAGE_PAIR_DIST;
					}
				}
//				loc-=20; //Search for overlapping read ends
//				assert(anchor.numericID<360000) : "loc="+loc+", searchDist="+searchDist+", idealStart="+idealStart+", searchIntoAnchor="+searchIntoAnchor+", maxMismatches="+maxMismatches;
//				System.err.println("loc="+loc+", searchDist="+searchDist+", idealStart="+idealStart+", searchIntoAnchor="+searchIntoAnchor+", maxMismatches="+maxMismatches);
				SiteScore ss=quickRescue(bases, ssa.chrom, strand, loc, searchDist+searchIntoAnchor, searchRight,
						idealStart, maxMismatches, POINTS_MATCH, POINTS_MATCH2);
				
				if(ss!=null && ss.isInBounds()){
					int mismatches=ss.slowScore;
					ss.setSlowScore(0);
					if(mismatches<=maxMismatches){
						slowRescue(bases, ss, maxLooseSwScore, maxImperfectScore, findRight, findLeft);
						if(ss.score>retainScoreLimit && ss.isInBounds()){
							if(ss.score>retainScoreLimit2){//Set them as paired to make them more resistant to being discarded
								ss.setPairedScore(Tools.max(ss.pairedScore, ss.slowScore+ssa.slowScore/4));
								ssa.setPairedScore(Tools.max(ssa.pairedScore, ssa.slowScore+ss.slowScore/4));
								assert(ss.pairedScore>0);
								assert(ssa.pairedScore>0);
							}
							loose.sites.add(ss);
						}
					}
				}
			}else{
				assert(ssa.pairedScore>0);
				assert(ssa.pairedScore>ssa.quickScore || ssa.pairedScore>ssa.slowScore) : ssa.toText();
			}
		}
	}
	
	
	final void slowRescue(final byte[] bases, SiteScore ss, final int maxScore, final int maxImperfectScore,
			boolean findTipDeletionsRight, boolean findTipDeletionsLeft){
		
		int swscoreNoIndel=msa.scoreNoIndels(bases, ss.chrom, ss.start());
		final int oldStart=ss.start();
		
		if(swscoreNoIndel<maxImperfectScore && MAX_INDEL>0){
			ss.setSlowScore(swscoreNoIndel);
			if(findTipDeletionsRight || findTipDeletionsLeft){
				boolean changed=findTipDeletions(ss, bases, maxImperfectScore, findTipDeletionsRight, findTipDeletionsLeft);
				if(changed){
					ss.match=null;
					swscoreNoIndel=msa.scoreNoIndels(bases, ss.chrom, ss.start());
				}
			}
			
			final int minMsaLimit=-CLEARZONE1e+(int)(MINIMUM_ALIGNMENT_SCORE_RATIO_PAIRED*maxScore);
			
			final int minscore=Tools.max(swscoreNoIndel, minMsaLimit);
			final int[] swscoreArray=msa.fillAndScoreLimited(bases, ss.chrom, ss.start(), ss.stop(), SLOW_RESCUE_PADDING, minscore, ss.gaps);
			
			if(swscoreArray!=null){
				ss.setSlowScore(swscoreArray[0]);
				ss.setScore(ss.slowScore);
				ss.setStart(swscoreArray[1]);
				ss.setStop(swscoreArray[2]);
				
				if(verbose){System.err.println("ss="+ss);}
				if(QUICK_MATCH_STRINGS && swscoreArray!=null && swscoreArray.length==6 && swscoreArray[0]>=minscore && (PRINT_SECONDARY_ALIGNMENTS || USE_SS_MATCH_FOR_PRIMARY)){
					assert(swscoreArray.length==6) : swscoreArray.length;
					assert(swscoreArray[0]>=minscore) : "\n"+Arrays.toString(swscoreArray)+"\n"+minscore;
					ss.match=msa.traceback(bases, Data.getChromosome(ss.chrom).array, ss.start()-SLOW_RESCUE_PADDING, ss.stop()+SLOW_RESCUE_PADDING,
							swscoreArray[3], swscoreArray[4], swscoreArray[5], ss.gaps!=null); //TODO: This failed once on a semiperfect low-complexity homo-5-mer sequence.
					if(ss.match!=null){
						ss.setLimits(swscoreArray[1], swscoreArray[2]);
						if(verbose){System.err.println("After quick match: ss="+ss+"\nbases="+new String(bases)+"\nref=  "+Data.getChromosome(ss.chrom).getString(ss.start, ss.stop));}
						assert(ss.lengthsAgree());
						ss.fixXY(bases, true, msa);
						ss.clipTipIndels(bases, 4, 10, msa);
						assert(ss.lengthsAgree());
						if(verbose){System.err.println("After clipping: ss="+ss);}
					}
				}else{ss.match=null;}
				
			}else{
				ss.setSlowScore(swscoreNoIndel);
				ss.setScore(ss.slowScore);
				ss.setStart(oldStart);
				ss.setStop(ss.start()+bases.length-1);
			}
		}else{
			ss.setSlowScore(swscoreNoIndel);
			ss.setScore(ss.slowScore);
			ss.setStop(ss.start()+bases.length-1);
		}
		ss.setPairedScore(ss.score+1);
		assert(ss.slowScore<=maxScore);
		ss.perfect=(ss.slowScore==maxScore);
		if(ss.perfect){ss.semiperfect=true;}
		else{ss.setPerfect(bases);}
	}
	
	
	protected static final void capSiteList(Read r, int cap, boolean printSecondary){
		if(r==null || r.sites==null || cap<0){return;}
		if(cap==0){r.sites=null;}
		else{
			for(int i=r.sites.size()-1; i>=cap; i--){r.sites.remove(i);}
		}
		if(!printSecondary || r.numSites()<2){return;}
		int max=r.topSite().slowScore;
		int min=Tools.min(max-500, (int)(max*SECONDARY_SITE_SCORE_RATIO));
		if(r.ambiguous()){//Ensures ambiguous reads will have at least one secondary site
			min=Tools.max(min, r.sites.get(1).score);
		}
		for(int i=r.sites.size()-1; i>0; i--){
			if(r.sites.get(i).slowScore<min){r.sites.remove(i);}
		}
//		assert(false) : r.mapScore+", "+max+", "+cap+", "+r.list;
//		assert(r.list.size()<2) : "\n"+max+", "+min+", "+r.list+"\n";
	}
	
	protected final static int removeDuplicateBestSites(Read r){
		int x=0;
		if(r.numSites()<2){return 0;}

		//Remove duplicate best sites that may exist as a result of realignment.
		final SiteScore ss1=r.topSite();
		for(int i=r.sites.size()-1; i>0; i--){
			SiteScore ss2=r.sites.get(i);
			if(ss1.chrom==ss2.chrom && ss1.strand==ss2.strand && ss1.start()==ss2.start() && ss1.stop()==ss2.stop()){
				if(!Shared.anomaly){
//					Shared.anomaly=true;
//					System.err.println("Ignoring anomalous duplicate site: "+"\n"+r.toText(false)+(r.mate==null ? "" : "\n"+r.mate.toText(false))+"\n");
					System.err.println("Ignoring anomalous duplicate site for rid="+r.numericID);
					Shared.anomaly=true;
//					new Exception().printStackTrace(System.err);
				}
				r.sites.remove(i);
				x++;
			}else{break;}
		}
		return x;
	}
	
	protected final static void removeUnmapped(ArrayList<Read> list){
		for(int i=0; i<list.size(); i++){
			Read r=list.get(i);
			if(r.numSites()==0){
				if(r.mate==null || r.mate.numSites()==0){
					list.set(i, null);
				}
			}
		}
	}
	
	protected final static void removeBlacklisted(ArrayList<Read> list){
		for(int i=0; i<list.size(); i++){
			Read r=list.get(i);
			if(Blacklist.inBlacklist(r)){
				list.set(i, null);
			}
		}
	}
	
	protected final static void removeMapped(ArrayList<Read> list){
		for(int i=0; i<list.size(); i++){
			Read r=list.get(i);
			if(r.numSites()==0){
				if(r.mate==null || r.mate.numSites()==0){
					list.set(i, null);
				}
			}
		}
	}
	
	
	public abstract int trimList(ArrayList<SiteScore> list, boolean retainPaired, int maxScore, boolean specialCasePerfect, int minSitesToRetain, int maxSitesToRetain);
	
	public final static int trimListAdvanced(ArrayList<SiteScore> list, boolean retainPaired, boolean retainSemiperfect, int maxScore, boolean specialCasePerfect,
			int minSitesToRetain, int maxSitesToRetain, boolean indexUsesExtendedScore, float thresh){
		if(list==null || list.size()==0){return -99999;}
		if(list.size()==1){return list.get(0).score;}
		
		final int highestScore;
		if(indexUsesExtendedScore){

			highestScore=Tools.trimSiteList(list, .6f, retainPaired, true, minSitesToRetain, maxSitesToRetain);
			if(highestScore==maxScore && specialCasePerfect){
				Tools.trimSiteList(list, .94f, retainPaired, true, minSitesToRetain, maxSitesToRetain);
				if(list.size()>8){Tools.trimSiteList(list, .99f, retainPaired, true, minSitesToRetain, maxSitesToRetain);}
				return highestScore;
			}

		}else{
			highestScore=Tools.trimSiteList(list, .4f, retainPaired, true, minSitesToRetain, maxSitesToRetain);
			thresh=thresh*0.5f;
		}

		int lim, lastScore=list.get(0).score;
		long area=lastScore;
		for(lim=1; lim<list.size(); lim++){
			SiteScore ss=list.get(lim);
			lastScore=ss.score;
			area=area+lastScore;
			if(lastScore<0 || (lastScore/(float)area)<thresh){break;}
		}
		lim=Tools.max(minSitesToRetain, lim);
		Tools.trimSitesBelowCutoff(list, lastScore, retainPaired, true, minSitesToRetain, maxSitesToRetain);
		
		return highestScore;
	}
	
	
	public abstract void scoreSlow(final ArrayList<SiteScore> list, final byte[] basesP, final byte[] basesM,
			final int maxSwScore, final int maxImperfectSwScore);
	
	/** This is only for saving ambiguous xy which is now irrelevant. */
	public final static boolean processAmbiguous(ArrayList<SiteScore> list, boolean primary, boolean removeAmbiguous, int clearzone, boolean save_xy){
		if(!save_xy){return true;}
		assert(false) : "TODO: Needs to be redone with contig names.";

		assert(list.size()>1);
		boolean ambiguous=true;
//		if(save_xy && minChrom<=24 && maxChrom>=24){
//			int best=list.get(0).score;
//
//			//Remove everything outside of the clearzone
//			for(int i=list.size()-1; i>0; i--){
//				assert(best>=list.get(i).score);
//				if(best-list.get(i).score>clearzone){
////					assert(i>1); //No longer true because of clearzone/clearzone2
//					list.remove(i);
//				}else{
////					assert(i>0); //Maybe no longer true because of clearzone/clearzone2
//					break;
//				}
//			}
//
//
//			assert(list.size()>1);
//			int Xcount=0;
//			int Ycount=0;
//			for(SiteScore ss : list){
//				assert(ss.score-list.get(0).score<=clearzone);
//				if(ss.chrom==23){
//					Xcount++;
//				}else if(ss.chrom==24){
//					Ycount++;
//				}
//			}
//			if(Xcount>1 || Ycount>2 || (Xcount+Ycount)<list.size()){
//				ambiguous=true;
//			}else{
//				ambiguous=false;
//				for(int i=list.size()-1; i>0; i--){list.remove(i);}
//				assert(list.size()==1);
//			}
//		}
		assert(list.size()>=1);

		if(ambiguous){
			assert(list.size()>1);
			if(removeAmbiguous){
				list.clear();
			}
		}
		
		return ambiguous;
	}
	
	int calcTrimmed(Read r){
		assert(UNTRIM && (TRIM_LEFT || TRIM_RIGHT));
		if(r==null || r.obj==null || r.obj.getClass()!=TrimRead.class){return 0;}
		TrimRead tr=(TrimRead) r.obj;
		return tr.trimmed();
	}
	
	public void calcStatistics1(final Read r, final int maxSwScore, final int maxPossibleQuickScore){
		final Read r2=r.mate;
		final int len1=r.length();
		final int len2=(r2==null ? 0 : r.length());
		
		if(OUTPUT_PAIRED_ONLY && r.mate!=null && !r.paired() && (r.mapped() || r.mate.mapped())){r.clearPairMapping();}
		if(r.ambiguous() && (AMBIGUOUS_TOSS || r.mapped())){
			ambiguousBestAlignment1++;
			ambiguousBestAlignmentBases1+=len1;
		}
		
		int trimmed=0;
		if((TRIM_LEFT || TRIM_RIGHT) && UNTRIM){
			trimmed=calcTrimmed(r)+calcTrimmed(r.mate);
		}
		if((!r.mapped() || (r.ambiguous() && AMBIGUOUS_TOSS)) && (r2==null || !r2.mapped() || (r2.ambiguous() && AMBIGUOUS_TOSS))){
			bothUnmapped+=r.pairCount();
			bothUnmappedBases+=r.pairLength()+trimmed;
		}else{
			eitherMapped+=r.pairCount();
			eitherMappedBases+=r.pairLength()+trimmed;
		}

		int[] correctness=calcCorrectness(r, THRESH);
		int correctGroup=correctness[0];
		int correctGroupSize=correctness[1];
		int numGroups=correctness[2];
		int elements=correctness[3];
		int correctScore=correctness[4];
		int topScore=correctness[5];
		int sizeOfTopGroup=correctness[6];
		int numCorrect=correctness[7];
		boolean firstElementCorrect=(correctness[8]==1);
		boolean firstElementCorrectLoose=(correctness[9]==1);
		boolean firstGroupCorrectLoose=(correctness[10]==1);

//		assert(firstElementCorrect) : "\n"+r.topSite()+"\n"+r.originalSite+"\n"+r.pairnum();
		
		assert(elements>0 == r.mapped());
		
		if(elements>0){
			
			if(r.match!=null){
				int[] errors=r.countErrors(SamLine.INTRON_LIMIT);
				matchCountM1+=errors[0];
				matchCountS1+=errors[1];
				matchCountD1+=errors[2];
				matchCountI1+=errors[3];
				matchCountN1+=errors[4];
				
				readCountS1+=(errors[1]>0 ? 1 : 0);
				readCountD1+=(errors[2]>0 ? 1 : 0);
				readCountI1+=(errors[3]>0 ? 1 : 0);
//				assert(errors[3]==0) : "\n"+r+"\n"+r2+"\n";
				readCountN1+=(errors[4]>0 ? 1 : 0);
				readCountSplice1+=(errors[5]>0 ? 1 : 0);
				readCountE1+=((errors[1]>0 || errors[2]>0 || errors[3]>0)? 1 : 0);
			}
			
			
			mappedRetained1++;
			mappedRetainedBases1+=len1;
			if(r.rescued()){
				if(r.strand()==Shared.PLUS){
					rescuedP1++;
				}else{
					rescuedM1++;
				}
			}
			if(r.paired()){
				numMated++;
				numMatedBases+=(len1+len2);
				int inner;
				int outer;
				if(r.start<=r2.start){
					inner=r2.start-r.stop;
					outer=r2.stop-r.start;
				}else{
					inner=r.start-r2.stop;
					outer=r.stop-r2.start;
				}

				inner=Tools.min(MAX_PAIR_DIST, inner);
				inner=Tools.max(MIN_PAIR_DIST, inner);
				innerLengthSum+=inner;
				outerLengthSum+=outer;
				insertSizeSum+=(inner+r.length()+r2.length());
			}else if(r2!=null && r2.mapped()/*&& r.list!=null && r.list.size()>0*/){
				badPairs++;
				badPairBases+=(len1+len2);
			}
			
			if(r.perfect() || (maxSwScore>0 && r.topSite().slowScore==maxSwScore)){
				perfectMatch1++;
				perfectMatchBases1+=len1;
			}else if(SLOW_ALIGN){
				assert(r.topSite().slowScore<maxSwScore) : maxSwScore+"\t"+r.topSite().toText();
			}
			
			int foundSemi=0;
			for(SiteScore ss : r.sites){
				if(ss.perfect){
					perfectHitCount1++;
					assert(ss.semiperfect);
				}
				if(ss.semiperfect){
					semiPerfectHitCount1++;
					foundSemi=1;
				}
			}
			semiperfectMatch1+=foundSemi;
			if(foundSemi>0){semiperfectMatchBases1+=len1;}
			
			if(firstElementCorrect){
				if(r.strand()==Shared.PLUS){firstSiteCorrectP1++;}
				else{firstSiteCorrectM1++;}
				if(r.paired()){firstSiteCorrectPaired1++;}
				else{firstSiteCorrectSolo1++;}
				if(r.rescued()){firstSiteCorrectRescued1++;}
			}else{
				firstSiteIncorrect1++;
//				System.out.println("********");
//				System.out.println(r.toText(false));
//				System.out.println(r2.toText(false));
			}
			
			if(firstElementCorrectLoose){
				firstSiteCorrectLoose1++;
			}else{
				firstSiteIncorrectLoose1++;
			}

			siteSum1+=elements;
			topSiteSum1+=sizeOfTopGroup;

			if(topScore==maxPossibleQuickScore){perfectHit1++;}
			if(sizeOfTopGroup==1){uniqueHit1++;}

			if(correctGroup>0){
				
				if(r.strand()==Shared.PLUS){truePositiveP1++;}
				else{truePositiveM1++;}
				totalCorrectSites1+=numCorrect;

				if(correctGroup==1){
					if(sizeOfTopGroup==1){
						correctUniqueHit1++;
					}else{
						correctMultiHit1++;
					}
				}else{
					correctLowHit1++;
				}

			}else{

				falsePositive1++;
//				System.out.println("********");
//				System.out.println(r.toText(false));
//				System.out.println(r2.toText(false));
			}
		}else if(maxPossibleQuickScore==-1){
			lowQualityReadsDiscarded1++;
			lowQualityBasesDiscarded1+=len1;
			r.setDiscarded(true);
		}else{
			noHit1++;
		}
	}
	
	
	public void calcStatistics2(final Read r, final int maxSwScore, final int maxPossibleQuickScore){
		final int len=r.length();
		
		if(r.ambiguous() && (AMBIGUOUS_TOSS || r.mapped())){
			ambiguousBestAlignment2++;
			ambiguousBestAlignmentBases2+=len;
		}
		
		int[] correctness=calcCorrectness(r, THRESH);
		int correctGroup=correctness[0];
		int correctGroupSize=correctness[1];
		int numGroups=correctness[2];
		int elements=correctness[3];
		int correctScore=correctness[4];
		int topScore=correctness[5];
		int sizeOfTopGroup=correctness[6];
		int numCorrect=correctness[7];
		boolean firstElementCorrect=(correctness[8]==1);
		boolean firstElementCorrectLoose=(correctness[9]==1);
		boolean firstGroupCorrectLoose=(correctness[10]==1);

//		assert(firstElementCorrect) : "\n"+r.topSite()+"\n"+r.originalSite+"\n"+r.pairnum();
		
		if(elements>0){
			
			if(r.match!=null){
				int[] errors=r.countErrors(SamLine.INTRON_LIMIT);
				matchCountM2+=errors[0];
				matchCountS2+=errors[1];
				matchCountD2+=errors[2];
				matchCountI2+=errors[3];
				matchCountN2+=errors[4];
				
				readCountS2+=(errors[1]>0 ? 1 : 0);
				readCountD2+=(errors[2]>0 ? 1 : 0);
				readCountI2+=(errors[3]>0 ? 1 : 0);
				readCountN2+=(errors[4]>0 ? 1 : 0);
				readCountSplice2+=(errors[5]>0 ? 1 : 0);
				readCountE2+=((errors[1]>0 || errors[2]>0 || errors[3]>0)? 1 : 0);
			}
			
			mappedRetained2++;
			mappedRetainedBases2+=len;
			if(r.rescued()){
				if(r.strand()==Shared.PLUS){
					rescuedP2++;
				}else{
					rescuedM2++;
				}
			}
			
			if(r.perfect() || (maxSwScore>0 && r.topSite().slowScore==maxSwScore)){
				perfectMatch2++;
				perfectMatchBases2+=len;
			}else if(SLOW_ALIGN){
				assert(r.topSite().slowScore<maxSwScore) : maxSwScore+"\t"+r.topSite().toText();
			}
			
			int foundSemi=0;
			for(SiteScore ss : r.sites){
				if(ss.perfect){
					perfectHitCount2++;
					assert(ss.semiperfect);
				}
				if(ss.semiperfect){
					semiPerfectHitCount2++;
					foundSemi=1;
				}
			}
			semiperfectMatch2+=foundSemi;
			if(foundSemi>0){semiperfectMatchBases2+=len;}

			if(firstElementCorrect){
				if(r.strand()==Shared.PLUS){firstSiteCorrectP2++;}
				else{firstSiteCorrectM2++;}
				if(r.paired()){firstSiteCorrectPaired2++;}
				else{firstSiteCorrectSolo2++;}
				if(r.rescued()){firstSiteCorrectRescued2++;}
			}else{
				firstSiteIncorrect2++;
//				System.out.println("********");
//				System.out.println(r.toText(false));
//				System.out.println(r.mate.toText(false));
			}
			
			if(firstElementCorrectLoose){
				firstSiteCorrectLoose2++;
			}else{
				firstSiteIncorrectLoose2++;
			}

			siteSum2+=elements;
			topSiteSum2+=sizeOfTopGroup;

			if(topScore==maxPossibleQuickScore){perfectHit2++;}
			if(sizeOfTopGroup==1){uniqueHit2++;}

			if(correctGroup>0){

				if(r.strand()==Shared.PLUS){truePositiveP2++;}
				else{truePositiveM2++;}
				totalCorrectSites2+=numCorrect;

				if(correctGroup==1){
					if(sizeOfTopGroup==1){
						correctUniqueHit2++;
					}else{
						correctMultiHit2++;
					}
				}else{
					correctLowHit2++;
				}

			}else{

				falsePositive2++;
//				System.out.println("********");
//				System.out.println(r.toText(false));
//				System.out.println(r.mate.toText(false));
			}
		}else if(maxPossibleQuickScore==-1){
			lowQualityReadsDiscarded2++;
			lowQualityBasesDiscarded2+=len;
		}else{
			noHit2++;
		}
	}
	
	public abstract void processRead(Read r, final byte[] basesM);
	
	@Deprecated
	protected final static boolean applyClearzone3_old(Read r, int CLEARZONE3, float INV_CLEARZONE3){
		
		assert(!r.paired()); //This is currently for unpaired reads
		if(!r.mapped() || r.ambiguous() || r.discarded() || r.numSites()<2){return false;}

		final int score1=r.topSite().slowScore;
		final int score2=r.sites.get(1).slowScore;
		final int score3=(r.sites.size()>2 ? r.sites.get(2).slowScore : -1);
		int dif=score1-score2;
		
		assert(r.mapScore==score1) : r.mapScore+", "+r.topSite().toText();

		assert(score1==r.mapScore);
		assert(score1>=score2) : "\n"+r.topSite().toText()+"\t<\t"+r.sites.get(1).toText()+"\n"+r.toText(false)+"\n";
		if(dif>=CLEARZONE3){return false;}

//		final int dif2=40+(CLEARZONE3-dif)/3;
//		final int dif2=(CLEARZONE3-dif)/2;
		int dif2=(CLEARZONE3-dif);
		
		float f=dif2*INV_CLEARZONE3;
		
		int sub=(dif2+2*(int)(f*dif2));
		
		if(score3!=-1){
			assert(score1>=score3);
			dif=score1-score3;
			assert(score1>=score3);
			if(dif<CLEARZONE3){
				dif2=(CLEARZONE3-dif);
				
				f=dif2*INV_CLEARZONE3;
				sub=sub+(dif2+2*(int)(f*dif2))/4;
				
//				sub=sub+(dif2)/2;
			}
		}
		
		for(SiteScore ss : r.sites){
			ss.setSlowScore(ss.slowScore-sub);
			ss.setScore(ss.score-sub);
		}
		r.mapScore-=sub;
		return sub>0;
	}
	
	
	protected final boolean applyClearzone3(Read r, int CLEARZONE3, float INV_CLEARZONE3){
		
		assert(!r.paired()); //This is currently for unpaired reads
		final ArrayList<SiteScore> list=r.sites;
		if(!r.mapped() || r.ambiguous() || r.discarded() || list==null || list.size()<2){return false;}

		final int score1=list.get(0).slowScore;
		assert(r.mapScore==score1) : r.mapScore+", "+list.get(0).toText()+"\n"+r;
		
		float sub=0;
		final int max=Tools.min(CZ3_MULTS.length, list.size());
		for(int i=1; i<max; i++){
			final SiteScore ss2=list.get(i);
			assert(ss2!=null) : r;
			if(ss2!=null){
				if(i>2 && ss2.slowScore<list.get(i-1).slowScore){break;}
//				final int score2=list.get(i).slowScore;
//				final int dif=score1-score2;
//				if(dif>=CLEARZONE3){break;}
//				int dif2=(CLEARZONE3-dif);
//				float f=dif2*INV_CLEARZONE3;
//				sub+=(dif2+2*(f*dif2))*CZ3_MULTS[i];
				float f=calcCZ3_fraction(score1, ss2.slowScore, CLEARZONE3, INV_CLEARZONE3);
				if(f<=0){break;}
				sub+=(f*CZ3_MULTS[i]);
			}
		}
		assert(sub>=0);
		if(sub<=0){return false;}
		
		float sub2;
//		float asymptote=8f+0.0267f*r.length();
		float asymptote=4f+0.03f*r.length();
		sub=sub*1.8f;
		sub2=CLEARZONE3*((asymptote*sub)/(sub+asymptote));
//		sub2=CLEARZONE3*sub;
//		System.out.println("sub="+sub+", sub2="+sub2+", CLEARZONE3="+CLEARZONE3+", (5*sub)="+(5*sub)+", (sub+5*CLEARZONE3)="+(sub+5*CLEARZONE3));
		int subi=(int)(sub2+0.5f);
		if(subi>=r.mapScore-300){
			subi=r.mapScore-300;
		}
		if(subi<=0){return false;}
		
		for(SiteScore ss : list){
			ss.setSlowScore(ss.slowScore-subi);
			ss.setScore(ss.score-subi);
		}
		r.mapScore-=subi;
		assert(r.mapScore>200);
		return true;
	}
	
	
//	protected float calcCZ3(int score1, int score2, int CLEARZONE3, float INV_CLEARZONE3){
//
//		int dif=score1-score2;
//		if(dif>=CLEARZONE3){return 0;}
//		//Now dif is between 0 and CZ3
//
////		final int dif2=40+(CLEARZONE3-dif)/3;
////		final int dif2=(CLEARZONE3-dif)/2;
//		int dif2=(CLEARZONE3-dif); //dif2 is higher if the scores are closer.
//
//		float f=dif2*INV_CLEARZONE3; //f ranges linearly from 1 (if the scores are identical) to 0 (when score2 is maximally below score1)
//
//		float f2=f*f;
//		float f7=(float)Math.pow(f, .7);
//
////		return (dif2+2f*f*dif2+2f*Tools.min(f2,0.5f)*dif2);
//		return (CLEARZONE3*f7+2f*f*dif2+2f*Tools.min(f2,0.5f)*dif2);
//	}
	
	
	protected float calcCZ3_fraction(int score1, int score2, int CLEARZONE3, float INV_CLEARZONE3){
		
		int dif=score1-score2;
		if(dif>=CLEARZONE3){return 0;}
		//Now dif is between 0 and CZ3

//		final int dif2=40+(CLEARZONE3-dif)/3;
//		final int dif2=(CLEARZONE3-dif)/2;
		int dif2=(CLEARZONE3-dif); //dif2 is higher if the scores are closer.
		
		float f=dif2*INV_CLEARZONE3; //f ranges linearly from 1 (if the scores are identical) to 0 (when score2 is maximally below score1)
		
		float f2=f*f;
//		float f7=(float)Math.pow(f, .7);
		
//		return (dif2+2f*f*dif2+2f*Tools.min(f2,0.5f)*dif2);
		return f+2f*f2+2f*f2*f;
	}
	
	/** Returns number of perfect pairs */
	public abstract int pairSiteScoresInitial(Read r, Read r2, boolean trim);


	
	

	protected static void pairSiteScoresFinal(Read r, Read r2, boolean trim, boolean setScore, int MAX_PAIR_DIST, int AVERAGE_PAIR_DIST,
			boolean SAME_STRAND_PAIRS, boolean REQUIRE_CORRECT_STRANDS_PAIRS, int maxTrimSitesToRetain){
		
		if(r.sites!=null){
			for(SiteScore ss : r.sites){ss.setPairedScore(0);}
		}
		if(r2.sites!=null){
			for(SiteScore ss : r2.sites){ss.setPairedScore(0);}
		}
		
		if(r.numSites()<1 || r2.numSites()<1){return;}
		
		SiteScore.PCOMP.sort(r.sites);
		SiteScore.PCOMP.sort(r2.sites);

		int maxPairedScore1=-1;
		int maxPairedScore2=-1;
		
		
//		if(verbose){
//			System.out.println(r.list.size()+", "+r2.list.size());
//			System.out.println();
//			for(SiteScore ss : r.list){
//				System.out.println(ss.toText());
//			}
//			System.out.println();
//			for(SiteScore ss : r2.list){
//				System.out.println(ss.toText());
//			}
//			System.out.println();
//		}
		
		final float mult1=Tools.min(1/2f, Tools.max(1/4f, (r.length()/(4f*r2.length()))));
		final float mult2=Tools.min(1/2f, Tools.max(1/4f, (r2.length()/(4f*r.length()))));
		
		final int ilimit=r.sites.size()-1;
		final int jlimit=r2.sites.size()-1;
		
		final int outerDistLimit=(Tools.max(r.length(), r2.length())*OUTER_DIST_MULT)/OUTER_DIST_DIV; //Minimum pairing distance
		final int expectedFragLength=AVERAGE_PAIR_DIST+r.length()+r2.length();
		
		if(verboseS){
			System.err.println("**************************   PAIRING   ********************************");
			System.err.println("outerDistLimit="+outerDistLimit+", MAX_PAIR_DIST="+MAX_PAIR_DIST);
		}
		
		for(int i=0, j=0; i<=ilimit && j<=jlimit; i++){
			SiteScore ss1=r.sites.get(i);
			SiteScore ss2=r2.sites.get(j);
			
			while(j<jlimit && (ss2.chrom<ss1.chrom || (ss2.chrom==ss1.chrom && ss1.start()-ss2.stop()>MAX_PAIR_DIST))){
				j++;
//				if(verbose){System.err.println("a.Incrementing j->"+j);}
				ss2=r2.sites.get(j);
			}

			for(int k=j; k<=jlimit; k++){
				ss2=r2.sites.get(k);
				
				if(verboseS){
					System.err.println("Considering sites:\n"+ss1+"\n"+ss2);
				}

				if(ss2.chrom>ss1.chrom){break;}
				//				if(verbose){System.err.println("Same chrom");}
				if(ss2.start()-ss1.stop()>MAX_PAIR_DIST){break;}

				final int innerdist;
				final int outerdist;
				
				//assert(!SAME_STRAND_PAIRS) : "TODO";
				
				if(REQUIRE_CORRECT_STRANDS_PAIRS){
					if(ss1.strand!=ss2.strand){
						if(ss1.strand==Shared.PLUS){
							innerdist=ss2.start()-ss1.stop();
							outerdist=ss2.stop()-ss1.start();
						}else{
							innerdist=ss1.start()-ss2.stop();
							outerdist=ss1.stop()-ss2.start();
						}
					}else{
						if(ss1.start()<=ss2.start()){
							innerdist=ss2.start()-ss1.stop();
							outerdist=ss2.stop()-ss1.start();
						}else{
							innerdist=ss1.start()-ss2.stop();
							outerdist=ss1.stop()-ss2.start();
						}
					}
				}else{
					if(ss1.start()<=ss2.start()){
						innerdist=ss2.start()-ss1.stop();
						outerdist=ss2.stop()-ss1.start();
					}else{
						innerdist=ss1.start()-ss2.stop();
						outerdist=ss1.stop()-ss2.start();
					}
				}
				
				if(verboseS){
					System.err.println("innerdist="+innerdist+", outerdist="+outerdist);
				}
				
//				if(ss1.start()<=ss2.start()){
//					innerdist=ss2.start()-ss1.stop();
//					outerdist=ss2.stop()-ss1.start();
//				}else{
//					innerdist=ss1.start()-ss2.stop();
//					outerdist=ss1.stop()-ss2.start();
//				}
				assert(outerdist>=innerdist) : "outerdist<innerdist:\n"+innerdist+", "+outerdist+", "+ss1+", "+ss2;
				
				if(outerdist>=outerDistLimit && innerdist<=MAX_PAIR_DIST){

					boolean strandOK=((ss1.strand==ss2.strand)==SAME_STRAND_PAIRS);
					//					if(verbose){System.err.println("strandOK="+strandOK);}

					if(strandOK || !REQUIRE_CORRECT_STRANDS_PAIRS){

						int deviation=absdif(AVERAGE_PAIR_DIST, innerdist);

						final int pairedScore1;
						final int pairedScore2;
						if(strandOK){
							//							pairedScore1=ss1.score+(int)(ss2.score*mult1);
							//							pairedScore2=ss2.score+(int)(ss1.score*mult2);

							pairedScore1=ss1.score+1+
									Tools.max(1, (int)(ss2.score*mult1)-(((deviation)*ss2.score)/Tools.max(100,(10*expectedFragLength+100))));
							pairedScore2=ss2.score+1+
									Tools.max(1, (int)(ss1.score*mult2)-(((deviation)*ss1.score)/Tools.max(100,(10*expectedFragLength+100))));
							
							
						}else{//e.g. a junction
							pairedScore1=ss1.score+ss2.score/16;
							pairedScore2=ss2.score+ss1.score/16;
						}
						
						if(verboseS){
							System.err.println("strandOK="+strandOK+"\tpairedScore1="+pairedScore1+", pairedScore2="+pairedScore2);
							System.err.println("             \tscore1="+ss1.score+", score2="+ss2.score);
						}
						
						ss1.setPairedScore(Tools.max(ss1.pairedScore, pairedScore1));
						ss2.setPairedScore(Tools.max(ss2.pairedScore, pairedScore2));
						maxPairedScore1=Tools.max(ss1.score, maxPairedScore1);
						maxPairedScore2=Tools.max(ss2.score, maxPairedScore2);
						//						if(verbose){System.err.println("Paired:\nss1="+ss1.toText()+", ss2="+ss2.toText());}
					}
				}else{
					//					if(verbose){System.err.println("Out of range");}
				}
			}
			//			if(verbose){System.err.println("\nss1="+ss1.toText()+", ss2="+ss2.toText());}
			
		}
		
		if(setScore){
			for(SiteScore ss : r.sites){
				if(ss.pairedScore>ss.score){ss.setScore(ss.pairedScore);}
				else{assert(ss.pairedScore==0);}
			}
			for(SiteScore ss : r2.sites){
				if(ss.pairedScore>ss.score){ss.setScore(ss.pairedScore);}
				else{assert(ss.pairedScore==0);}
			}
		}
		
		if(trim){
//			Tools.trimSitesBelowCutoffInplace(r.list, (int)(maxPairedScore1*.95f), false);
//			Tools.trimSitesBelowCutoffInplace(r2.list, (int)(maxPairedScore2*.95f), false);
			float f=Tools.min(SECONDARY_SITE_SCORE_RATIO, 0.95f);
			Tools.trimSitesBelowCutoff(r.sites, (int)(maxPairedScore1*f), false, true, 1, maxTrimSitesToRetain);
			Tools.trimSitesBelowCutoff(r2.sites, (int)(maxPairedScore2*f), false, true, 1, maxTrimSitesToRetain);
		}
	}
	
	protected final static boolean canPair(SiteScore ss1, SiteScore ss2, int len1, int len2,
			boolean REQUIRE_CORRECT_STRANDS_PAIRS, boolean SAME_STRAND_PAIRS, int MAX_PAIR_DIST){
		if(ss1.chrom!=ss2.chrom){return false;}
		if(REQUIRE_CORRECT_STRANDS_PAIRS){
			boolean strandOK=((ss1.strand==ss2.strand)==SAME_STRAND_PAIRS);
			if(!strandOK){return false;}
		}
//		int dist=0;
//
//		if(ss1.start()<=ss2.start()){
//			dist=ss2.start()-ss1.stop();
//		}else if(ss1.start()>ss2.start()){
//			dist=ss1.start()-ss2.stop();
//		}
//
//		return (dist>=MIN_PAIR_DIST && dist<=MAX_PAIR_DIST);
		
//		final int outerDistLimit=MIN_PAIR_DIST+len1+len2;
//		final int outerDistLimit=(Tools.max(len1, len2)*(OUTER_DIST_MULT2))/OUTER_DIST_DIV;
		final int outerDistLimit=(Tools.max(len1, len2)*(OUTER_DIST_MULT))/OUTER_DIST_DIV;
		int innerdist=0;
		int outerdist=0;
		
		if(verboseS){
			System.err.println("canPair: outerDistLimit="+outerDistLimit);
		}
		
//		if(ss1.start()<=ss2.start()){
//			innerdist=ss2.start()-ss1.stop();
//			outerdist=ss2.stop()-ss1.start();
//		}else if(ss1.start()>ss2.start()){
//			innerdist=ss1.start()-ss2.stop();
//			outerdist=ss1.stop()-ss2.start();
//		}
//		assert(outerdist>=innerdist);
		
		//assert(!SAME_STRAND_PAIRS) : "TODO";
		
		if(REQUIRE_CORRECT_STRANDS_PAIRS){
			if(ss1.strand!=ss2.strand){
				if(ss1.strand==Shared.PLUS){
					innerdist=ss2.start()-ss1.stop();
					outerdist=ss2.stop()-ss1.start();
				}else{
					innerdist=ss1.start()-ss2.stop();
					outerdist=ss1.stop()-ss2.start();
				}
			}else{
				if(ss1.start()<=ss2.start()){
					innerdist=ss2.start()-ss1.stop();
					outerdist=ss2.stop()-ss1.start();
				}else{
					innerdist=ss1.start()-ss2.stop();
					outerdist=ss1.stop()-ss2.start();
				}
			}
		}else{
			if(ss1.start()<=ss2.start()){
				innerdist=ss2.start()-ss1.stop();
				outerdist=ss2.stop()-ss1.start();
			}else{
				innerdist=ss1.start()-ss2.stop();
				outerdist=ss1.stop()-ss2.start();
			}
		}
		
		return (outerdist>=outerDistLimit && innerdist<=MAX_PAIR_DIST);
	}
	
	
//	/** Returns the number of additional bases away that should be searched for slow align.
//	 * This should probably be called between quickMap and slowAlign, only on
//	 * sites where stop-start<=bases.length-1 */
//	public abstract void findTipDeletions(final Read r, final byte[] basesP, final byte[] basesM, final int maxSwScore, final int maxImperfectScore);
//
//	public abstract boolean findTipDeletions(SiteScore ss, final byte[] bases, final int maxImperfectScore, boolean lookRight, boolean lookLeft);
	
	
	/** Returns the number of additional bases away that should be searched for slow align.
	 * This should probably be called between quickMap and slowAlign, only on
	 * sites where stop-start<=bases.length-1 */
	protected final static int findTipDeletionsRight(final byte[] bases, final int chrom,
			int originalStop, int searchDist, int tiplen){
		ChromosomeArray cha=Data.getChromosome(chrom);
		byte[] ref=cha.array;
		if(originalStop<cha.minIndex+tiplen-1){return 0;} //fail
		
		int minMismatches=tiplen;
		int bestStart=originalStop;
		
		final int tipCoord=bases.length-1;
		
		int lastMismatch=0;
		int originalMismatches=0;
		int contig=0;
		for(int i=0; i<tiplen && contig<5; i++){
			if(bases[tipCoord-i]!=ref[originalStop-i]){
				originalMismatches++;
				lastMismatch=i;
				contig=0;
			}else{
				contig++;
			}
		}
//		System.err.print("!");
		if(originalMismatches<3){return 0;}
		minMismatches=originalMismatches;
		tiplen=lastMismatch+1;
		assert(tiplen>1);
		if(tiplen<4){return 0;}
//		System.err.println("Tiplen="+tiplen+", mismatches="+originalMismatches);
//		System.err.print("* ");
		
		searchDist=Tools.min(searchDist, 30*originalMismatches);
		int lastIndexToStart=Tools.min(ref.length-1, originalStop+searchDist);
		for(int start=originalStop+1; start<=lastIndexToStart && minMismatches>0; start++){
//			System.err.print("_");
			int mismatches=0;
			for(int j=0; j<tiplen && mismatches<minMismatches; j++){
				if(bases[tipCoord-j]!=ref[start-j]){
					mismatches++;
				}
			}
//			System.err.print(mismatches+" ");
			if(mismatches<minMismatches){
				bestStart=start;
				minMismatches=mismatches;
			}
		}
//		System.err.println("\noriginalStop+1:"+(originalStop+1)+"\nlastIndexToStart:"+(lastIndexToStart)+"\ntiplen: "+tiplen+"\noriginalMismatches: "+originalMismatches+"\nminMismatches: "+minMismatches+"\n");
		if(minMismatches>2 || originalMismatches-minMismatches<2){
			return 0;
		}
//		System.err.println(" $$$ ");
		return bestStart-originalStop;
	}
	
	
	/** Returns the number of additional bases away that should be searched for slow align.
	 * This should probably be called between quickMap and slowAlign, only on
	 * sites where stop-start<=bases.length-1 */
	protected final static int findTipDeletionsLeft(final byte[] bases, final int chrom,
			final int originalStart, int searchDist, int tiplen){
		ChromosomeArray cha=Data.getChromosome(chrom);
		byte[] ref=cha.array;
		if(originalStart+tiplen>=ref.length){return 0;} //fail
		
		if(cha.minIndex>=originalStart){return 0;} //fail
		
		int minMismatches=tiplen;
		int bestStart=originalStart;
		
		int lastMismatch=0;
		int originalMismatches=0;
		int contig=0;
		for(int i=0; i<tiplen && contig<5; i++){
			if(bases[i]!=ref[originalStart+i]){
				originalMismatches++;
				lastMismatch=i;
				contig=0;
			}else{
				contig++;
			}
		}
//		System.err.print("!");
		if(originalMismatches<3){return 0;}
		minMismatches=originalMismatches;
		tiplen=lastMismatch+1;
		assert(tiplen>1);
		if(tiplen<4){return 0;}
//		System.err.println("Tiplen="+tiplen+", mismatches="+originalMismatches);
//		System.err.print("* ");
		
		searchDist=Tools.min(searchDist, 16+16*originalMismatches+8*tiplen);
		int lastIndexToStart=Tools.max(cha.minIndex, originalStart-searchDist);
		for(int start=originalStart-1; start>=lastIndexToStart && minMismatches>0; start--){
//			System.err.print("_");
			int mismatches=0;
			for(int j=0; j<tiplen && mismatches<minMismatches; j++){
				if(bases[j]!=ref[start+j]){
					mismatches++;
				}
			}
//			System.err.print(mismatches+" ");
			if(mismatches<minMismatches){
				bestStart=start;
				minMismatches=mismatches;
			}
		}
//		System.err.println("\noriginalStop+1:"+(originalStop+1)+"\nlastIndexToStart:"+(lastIndexToStart)+"\ntiplen: "+tiplen+"\noriginalMismatches: "+originalMismatches+"\nminMismatches: "+minMismatches+"\n");
		if(minMismatches>2 || originalMismatches-minMismatches<2){
			return 0;
		}
//		System.err.println(" $$$ ");
		return originalStart-bestStart;
	}
	
	
//	public abstract void rescue(Read anchor, Read loose, byte[] basesP, byte[] basesM, int searchDist);
	
	
//	public abstract void slowRescue(final byte[] bases, SiteScore ss, final int maxScore, final int maxImperfectScore,
//			boolean findTipDeletionsRight, boolean findTipDeletionsLeft);
	
	
	/** Assumes bases are already on the correct strand */
	public final SiteScore quickRescue(final byte[] bases, final int chrom, final byte strand, final int loc, final int searchDist,
			final boolean searchRight, final int idealStart, final int maxAllowedMismatches, int POINTS_MATCH, int POINTS_MATCH2){
		if(bases==null || bases.length<10){return null;}
		ChromosomeArray cha=Data.getChromosome(chrom);
		byte[] ref=cha.array;
		
		int lowerBound, upperBound;
		if(searchRight){
			lowerBound=Tools.max(cha.minIndex, loc);
			upperBound=Tools.min(ref.length-bases.length, loc+searchDist);
		}else{
			lowerBound=Tools.max(cha.minIndex, loc-searchDist);
			upperBound=Tools.min(ref.length-bases.length, loc);
		}
//		assert(false) : lowerBound+", "+upperBound;
//		int minMismatches=(int)(bases.length*.6f); //Default: .75f.  Lower numbers are faster with lower quality.
		int minMismatches=maxAllowedMismatches+1;
		//For situations like RNASEQ with lots of deletions, a higher value of at least .75 should be used.
		
		int maxContigMatches=0;
		int bestScore=0;
		int bestStart=-1;
		int bestAbsdif=Integer.MAX_VALUE;
		
		if(searchRight){
			for(int start=lowerBound; start<=upperBound/* && minMismatches>0*/; start++){
				int mismatches=0;
				int contig=0;
				int currentContig=0;
				for(int j=0; j<bases.length && mismatches<=minMismatches; j++){
					final byte c=bases[j], r=ref[start+j];
					if(c!=r || c=='N'){
						mismatches++;
						contig=Tools.max(contig, currentContig);
						currentContig=0;
					}else{
						currentContig++;
					}
				}
				
				int score=(bases.length-mismatches)+contig;
				int absdif=absdif(start, idealStart);
				if(mismatches<=minMismatches && (score>bestScore || (score==bestScore && absdif<bestAbsdif))){
					bestStart=start;
					minMismatches=mismatches;
					maxContigMatches=contig;
					bestScore=score;
					bestAbsdif=absdif;
					if(mismatches==0){upperBound=Tools.min(upperBound, idealStart+absdif);}
//					assert(upperBound>=start && lowerBound<=start);
//					assert(upperBound>=idealStart);
//					assert(lowerBound<=idealStart);
				}
			}
		}else{
			for(int start=upperBound; start>=lowerBound/* && minMismatches>0*/; start--){
				int mismatches=0;
				int contig=0;
				int currentContig=0;
				for(int j=0; j<bases.length && mismatches<=minMismatches; j++){
					final byte c=bases[j], r=ref[start+j];
					if(c!=r || c=='N'){
						mismatches++;
						contig=Tools.max(contig, currentContig);
						currentContig=0;
					}else{
						currentContig++;
					}
				}

				int score=(bases.length-mismatches)+contig;
				int absdif=absdif(start, idealStart);
				if(mismatches<=minMismatches && (score>bestScore || (score==bestScore && absdif<bestAbsdif))){
					bestStart=start;
					minMismatches=mismatches;
					maxContigMatches=contig;
					bestScore=score;
					bestAbsdif=absdif;
					if(mismatches==0){lowerBound=Tools.max(lowerBound, idealStart-absdif);}
//					assert(upperBound>=start && lowerBound<=start);
//					assert(upperBound>=idealStart);
//					assert(lowerBound<=idealStart);
				}
			}
		}
		
		if(bestStart<0){return null;}
		
		//These scores are dummies and will not quite match the normally generated scores.
		final int scoreOut;
		if(USE_AFFINE_SCORE){
			scoreOut=POINTS_MATCH+(POINTS_MATCH2*(bases.length-1-minMismatches));
		}else{
			scoreOut=maxContigMatches+(BASE_HIT_SCORE*(bases.length-minMismatches));
		}
		
		SiteScore ss=new SiteScore(chrom, strand, bestStart, bestStart+bases.length-1, 0, scoreOut);
		ss.setPerfect(bases);
		ss.rescued=true;
		ss.setSlowScore(minMismatches); //TODO: Clear this field later!
		return ss;
	}
	
	
	/** Assumes bases are already on the correct strand */
	protected final static int[] quickerRescue(final byte[] bases, final int chrom, int loc, final int searchDist){
		ChromosomeArray cha=Data.getChromosome(chrom);
		byte[] ref=cha.array;
		if(loc<cha.minIndex){loc=cha.minIndex;}
		
		int lastIndexToStart=loc+searchDist-1;
		final int limit=Tools.min(lastIndexToStart, ref.length-bases.length)+1;

		int minMismatches=bases.length;
		int bestStart=-1;
		for(int start=loc; start<limit && minMismatches>0; start++){
			int mismatches=0;
			for(int j=0; j<bases.length && mismatches<minMismatches; j++){
				if(bases[j]!=ref[start+j]){
					mismatches++;
				}
			}
			if(mismatches<minMismatches){
				bestStart=start;
				minMismatches=mismatches;
			}
		}
		
		return new int[] {bestStart, bestStart+bases.length-1, minMismatches};
	}
	
	
	public abstract void processReadPair(final Read r, final byte[] basesM1, final byte[] basesM2);
	
	/** TODO: Iterate through loop backwards when removing sites.
	 * @param r
	 * @param DONT_OUTPUT_UNMAPPED_READS
	 * @param SAM_OUT
	 * @param EXPECTED_LEN_LIMIT
	 * @return Number of sites removed
	 */
	protected final static int removeOutOfBounds(Read r, boolean DONT_OUTPUT_UNMAPPED_READS, boolean SAM_OUT, int EXPECTED_LEN_LIMIT){
//		assert(false) : DONT_OUTPUT_UNMAPPED_READS+", "+SAM_OUT+", "+EXPECTED_LEN_LIMIT;
		ArrayList<SiteScore> ssl=r.sites;
		if(ssl==null){return 0;}
		int initial=ssl.size();
		for(int i=0; i<ssl.size(); i++){
			SiteScore ss=ssl.get(i);
//			System.out.println("Estimated greflen: "+GapTools.calcGrefLen(ss.start(), ss.stop(), ss.gaps));
			ChromosomeArray cha=Data.getChromosome(ss.chrom);
			int max=cha.maxIndex;
			if(ss.start()<0 || ss.stop()>max){
				ssl.remove(i);
				i--;
				ss=null;
			}else if(/*DONT_OUTPUT_UNMAPPED_READS && */SAM_OUT){
				if(!Data.isSingleScaffold(ss.chrom, ss.start(), ss.stop())){
					//TODO: Attempt to trim instead of removing
					ssl.remove(i);
					i--;
					ss=null;
				}
			}
			if(ss!=null){
				int expectedLen=GapTools.calcGrefLen(ss);
				if(expectedLen>=EXPECTED_LEN_LIMIT){
					//TODO: Alternately, I could kill the site.
					ss.setStop(ss.start()+Tools.min(r.length()+40, EXPECTED_LEN_LIMIT));
					if(ss.gaps!=null){GapTools.fixGaps(ss);}
				}
			}
		}
		
//		System.out.println("Estimated greflen: "+GapTools.calcGrefLen(r.start, r.stop, r.gaps));
//		assert(false);
		
		return initial-ssl.size();
	}
	
	protected static final int forbidSelfMapping(ArrayList<SiteScore> ssl, SiteScore original){
//		assert(original!=null);
		if(ssl==null || ssl.isEmpty() || original==null){return 0;}
		int removed=0;
		for(int i=0; i<ssl.size(); i++){
			SiteScore ss=ssl.get(i);
			if(ss.overlaps(original, true)){
				ssl.set(i, null);
				removed++;
			}
		}
		if(removed>0){Tools.condenseStrict(ssl);}
		return removed;
	}
	

	/** Generate a score penalty based on the presence of errors near the read tips. */
	public static int calcTipScorePenalty(final Read r, final int maxScore, final int tiplen){
		if(!r.mapped() || r.match==null || r.length()<2*tiplen){return 0;}
		
		int points=0;
		final byte[] match=r.match;
		final byte[] bases=r.bases;
		final int last=r.length()-1;
		byte prev='m';
		for(int i=0, cpos=0; cpos<=tiplen; i++){
			byte b=match[i];
			if(b=='m'){
				cpos++;
			}else if(b=='D'){
				if(prev!='D'){points+=2*(tiplen+2-cpos);}
			}else if(b=='N' || b=='C'){
				points+=(tiplen+2-cpos);
				cpos++;
			}else{
				if(Tools.isDigit(b)){
					r.toLongMatchString(false);
					return calcTipScorePenalty(r, maxScore, tiplen);
				}
				assert(b=='I' || b=='S') : ((char)b)+"\n"+new String(match)+"\n"+new String(bases)+"\n";
				points+=2*(tiplen+2-cpos);
				cpos++;
			}
			prev=b;
		}
		
		prev='m';
		for(int i=match.length-1, cpos=0; cpos<=tiplen; i--){
			byte b=match[i];
			if(b=='m'){
				cpos++;
			}else if(b=='D'){
				if(prev!='D'){points+=2*(tiplen+2-cpos);}
			}else if(b=='N' || b=='C'){
				points+=(tiplen+2-cpos);
				cpos++;
			}else{
				assert(b=='I' || b=='S');
				points+=2*(tiplen+2-cpos);
				cpos++;
			}
			prev=b;
		}
		
		byte b=bases[0];
		//homopolymer tip penalty
		if(b!='N' && b==bases[1]){
			for(int i=2; i<=tiplen && bases[i]==b; i++){points++;}
		}
		
		//homopolymer tip penalty
		b=bases[last];
		if(b!='N' && b==bases[last-1]){
			for(int i=last-2; i>=(last-tiplen) && bases[i]==b; i--){points++;}
		}
		
		//Did not seem to help
//		int hits=r.list.get(0).hits;
//		float desired=Tools.min(6, bases.length/12f);
//		if(hits<desired){points+=20*(1-(hits/desired));}
		
		if(points<1){return 0;}
//		points=Tools.min(points, 40);
		
		float asymptote=80;
		float f=((asymptote*points)/(points+asymptote));
		
		int penalty=(int)(f*.0022f*maxScore);
		int maxPenalty=r.mapScore-maxScore/10;
		if(maxPenalty<=0){return 0;}
		return Tools.min(penalty, maxPenalty);
		
//		final int len=7;
//		int dist1=len+1, dist2=len+1;
//		for(int i=0; i<=len; i++){
//			if(r.match[i]!='m'){
//				dist1=i;
////				System.out.println("dist1="+dist1+"\n"+new String(r.match));
//				break;
//			}
//		}
//		for(int i=0, tip=r.match.length-1; i<=len; i++){
//			if(r.match[tip-i]!='m'){
//				dist2=i;
////				System.out.println("dist2="+dist2+"\n"+new String(r.match));
//				break;
//			}
//		}
//		float penalty=0;
//		if(dist1<len){
//			penalty+=(len-dist1+1)*.005f*maxScore;
//		}
//		if(dist2<len){
//			penalty+=(len-dist2+1)*.005f*maxScore;
//		}
//		return (int)penalty;
	}
	
	
	public static void applyScorePenalty(Read r, int penalty){
		if(penalty>0){
			r.mapScore-=penalty;
			for(SiteScore ss : r.sites){
				ss.setSlowScore(ss.slowScore-penalty);
				ss.setScore(ss.score-penalty);
			}
		}
	}
	
	
	/** {group of correct hit (or -1), size of correct group, number of groups,
	 * number of elements, correctScore, maxScore, size of top group, num correct, firstElementCorrect,
	 * firstElementCorrectLoose, firstGroupCorrectLoose} */
	protected int[] calcCorrectness(Read r, int thresh){
		//assume sorted.
		ArrayList<SiteScore> ssl=r.sites;
		
		if(ssl==null || ssl.isEmpty()){
			return new int[] {-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
		}

		SiteScore original=r.originalSite;
		assert((original==null) != (r.synthetic()));
		if(original==null){
			original=ssl.get(0);
		}
		
		int group=0;
		int correctGroup=-1;
		int groupSize=0;
		int correctGroupSize=-1;
		int prevScore=Integer.MAX_VALUE;
		int sizeOfTopGroup=0;
		SiteScore correct=null;

		int firstElementCorrect=0;
		int firstElementCorrectLoose=0;
		int firstGroupCorrectLoose=0;
		
		int numCorrect=0;
		
		for(int i=0; i<ssl.size(); i++){
			SiteScore ss=ssl.get(i);
			if(ss.score==ssl.get(0).score){sizeOfTopGroup++;}
			
			if(prevScore!=ss.score){
				assert(prevScore>ss.score || (AMBIGUOUS_RANDOM && r.ambiguous()) || r.mate!=null) : "prevScore="+prevScore+", score="+ss.score+
					", i="+i+", r="+r+"\n\nss"+i+" = "+ss+"\n\n"+(i==0 ? "" : "ss"+(i-1)+" = "+ssl.get(i-1));
				
				if(correctGroup==group){
					correctGroupSize=groupSize;
				}
				
				group++;
				groupSize=0;
				prevScore=ss.score;
			}
			groupSize++;
			

//			boolean b=isCorrectHit(ss, original.chrom, original.strand, original.start, 1, thresh);
			boolean b=isCorrectHit(ss, original.chrom, original.strand, original.start(), original.stop(), thresh);
			boolean b2=isCorrectHitLoose(ss, original.chrom, original.strand, original.start(), original.stop(), thresh+20);
//			assert(false) : b+", "+b2+"\n"+ss+"\n"+original+"\n"+ss.chrom+", "+ss.strand+", "+ss.start+", "+ss.stop;
			if(b){
				if(i==0){firstElementCorrect=1;}
				numCorrect++;
				if(correct==null){
					correct=ss;
					correctGroup=group;
				}
			}
			if(b2){
				if(i==0){firstElementCorrectLoose=1;}
				if(group==0){firstGroupCorrectLoose=1;}
			}
		}
		if(correctGroup==group){
			correctGroupSize=groupSize;
		}

		assert(correctGroup!=0 && correctGroup<=group);
		assert(group<=ssl.size());
		assert(sizeOfTopGroup>0 && sizeOfTopGroup<=ssl.size());
		assert((correctGroup>0) == (correctGroupSize>0));
		return new int[] {correctGroup, correctGroupSize, group, ssl.size(),
				correct==null ? 0 : correct.score, ssl.get(0).score, sizeOfTopGroup, numCorrect, firstElementCorrect,
						firstElementCorrectLoose, firstGroupCorrectLoose};
	}
	
	
	public static final boolean isCorrectHit(SiteScore ss, int trueChrom, byte trueStrand, int trueStart, int trueStop, int thresh){
//		boolean b=(ss.chrom==trueChrom && ss.strand==trueStrand);
		if(ss.chrom!=trueChrom || ss.strand!=trueStrand){return false;}

		assert(ss.stop()>ss.start()) : ss.toText()+", "+trueStart+", "+trueStop;
		assert(trueStop>trueStart) : ss.toText()+", "+trueStart+", "+trueStop;

		return (absdif(ss.start(), trueStart)<=thresh && absdif(ss.stop(), trueStop)<=thresh);
//		return (absdif(ss.start(), trueStart)<=thresh || absdif(ss.stop(), trueStop)<=thresh);
		
//		if(absdif(ss.start(), trueStart)<=thresh){return true;}
//		if(absdif(ss.stop(), trueStop)<=thresh){return true;}
//		return false;
		
//		if(absdif(ss.start(), trueStart)>thresh){return false;}
//		if(absdif(ss.stop(), trueStop)>thresh){return false;}
//		return true;
	}
	
	
	public static final boolean isCorrectHitLoose(SiteScore ss, int trueChrom, byte trueStrand, int trueStart, int trueStop, int thresh){
//		boolean b=(ss.chrom==trueChrom && ss.strand==trueStrand);
		if(ss.chrom!=trueChrom || ss.strand!=trueStrand){return false;}

		assert(ss.stop()>ss.start()) : ss.toText()+", "+trueStart+", "+trueStop;
		assert(trueStop>trueStart) : ss.toText()+", "+trueStart+", "+trueStop;
		
		return (absdif(ss.start(), trueStart)<=thresh || absdif(ss.stop(), trueStop)<=thresh);
		
//		if(absdif(ss.start(), trueStart)<=thresh){return true;}
//		if(absdif(ss.stop(), trueStop)<=thresh){return true;}
//		return false;
		
//		if(absdif(ss.start(), trueStart)>thresh){return false;}
//		if(absdif(ss.stop(), trueStop)>thresh){return false;}
//		return true;
	}
	
	protected static final byte[] makePerfectMatchString(int len){
		byte[] r=new byte[len];
		Arrays.fill(r, (byte)'m');
		return r;
	}
	
	protected static final int absdif(int a, int b){
		return a>b ? a-b : b-a;
	}
	
	/** Returns maximum read length supported by this mapper */
	public abstract int maxReadLength();
	
	/** Ensure top site is congruent with read */
	protected static final boolean checkTopSite(Read r){
		if(!r.mapped()){return true;}
		if(r.numSites()==0){return false;}
		SiteScore ss=r.topSite();
		if(ss==null){return false;}
		boolean b=(ss.start()==r.start) && (ss.stop()==r.stop) && (ss.strand==r.strand()) && (ss.chrom==r.chrom) && (ss.match==r.match);
		assert(b) : "\nread="+r+"\nmate="+r.mate+"\nss="+ss+"\n"+(ss==null ? "ss is null" :
			((ss.start()==r.start)+", "+(ss.stop()==r.stop)+", "+(ss.strand==r.strand())+", "+(ss.chrom==r.chrom)+", "+(ss.match==r.match))+"\nlist="+r.sites);
		return b;
	}
	
	
	protected static final int removeLongIndels(ArrayList<SiteScore> list, int maxlen){
		if(list==null || list.size()<1){return 0;}
		int removed=0;
		for(int i=list.size()-1; i>=0; i--){
			SiteScore ss=list.get(i);
			if(hasLongIndel(ss.match, maxlen)){
				list.remove(i);
				removed++;
			}
		}
		return removed;
	}
	
	protected static final boolean hasLongIndel(byte[] match, int maxlen){
		if(match==null || match.length<maxlen){return false;}
		byte prev='0';
		int len=0;
		for(byte b : match){
			if(b=='D' || b=='I' || b=='X' || b=='Y'){
				if(b==prev){len++;}
				else{len=1;}
				if(len>maxlen){return true;}
			}else{
				len=0;
			}
			prev=b;
		}
		return false;
	}
	
	/** TODO */
	final void processReadSplit(Read r, byte[] basesM, int minlen, int maxlen){
		assert(minlen>=KEYLEN && maxlen>=minlen) : KEYLEN+", "+maxlen+", "+minlen;
		int len=r.length();
		if(len<=maxlen){
			processRead(r, basesM);
			return;
		}
		ArrayList<Read> subreads=r.split(minlen, maxlen);
	}
	
	public final synchronized boolean finished(){return finished;}
	
	public final synchronized boolean working(){return !finished;}
	
	final synchronized void finish(){
		assert(!finished);
		finished=true;
		notifyAll();
	}
	
	private boolean finished=false;
	
	private static final float[] CZ3_MULTS=new float[] {0f, 1f, .75f, 0.5f, 0.25f, 0.125f, 0.0625f};
	
	/*--------------------------------------------------------------*/
	
	/** Input read source. */
	protected final ConcurrentReadInputStream cris;

	
	/** All reads go here. <br>
	 * If outputunmapped=false, omit unmapped single reads and double-unmapped paired reads. */
	protected final ConcurrentReadOutputStream outStream;
	/** All mapped reads (and half-mapped pairs) go here except reads that only map to the blacklist. */
	protected final ConcurrentReadOutputStream outStreamMapped;
	/** All unmapped reads (and double-unmapped pairs) go here. */
	protected final ConcurrentReadOutputStream outStreamUnmapped;
	/** All reads (and half-mapped pairs) that map best to the blacklist go here. */
	protected final ConcurrentReadOutputStream outStreamBlack;
	
	
	/*--------------------------------------------------------------*/
	
	
	public final String MSA_TYPE;
	final MSA msa;
	public final ReadStats readstats;
	public final CoveragePileup pileup;
	public final int POINTS_MATCH, POINTS_MATCH2;
	public final int KEYLEN;
	
	protected final boolean PERFECTMODE; //Only look for perfect matches
	protected final boolean SEMIPERFECTMODE; //Only look for perfect and semiperfect matches
	protected final boolean FORBID_SELF_MAPPING; //Do not allow reads to map to their official origin.  Allows you to find next-best matches (when supported)
	protected final boolean RCOMP_MATE; //Reverse-complement mate prior to mapping
	protected static boolean RCOMP=false;
	/** True if this thread should generate a match string for the best match */
	protected final boolean MAKE_MATCH_STRING;
	
	protected final boolean OUTPUT_MAPPED_ONLY;
	protected final boolean DONT_OUTPUT_BLACKLISTED_READS;
	protected final boolean PRINT_SECONDARY_ALIGNMENTS;
	protected final boolean QUICK_MATCH_STRINGS;
	protected final boolean USE_SS_MATCH_FOR_PRIMARY=true;

	protected final int MAX_SITESCORES_TO_PRINT;
	
	/** Scores below the (max possible alignment score)*(MINIMUM_ALIGNMENT_SCORE_RATIO) will be discarded.
	 * Default: 0.4 for synthetic data. */
	protected final float MINIMUM_ALIGNMENT_SCORE_RATIO;
	protected final float MINIMUM_ALIGNMENT_SCORE_RATIO_PRE_RESCUE;
	protected final float MINIMUM_ALIGNMENT_SCORE_RATIO_PAIRED;

	protected final float keyDensity;
	protected final float maxKeyDensity;
	protected final float minKeyDensity;
	protected final int maxDesiredKeys;
	
	/*--------------------------------------------------------------*/

	final int CLEARZONE1e;
	
	/*--------------------------------------------------------------*/
	
	final int MIN_APPROX_HITS_TO_KEEP;
	final boolean USE_EXTENDED_SCORE;
	public static final boolean GENERATE_BASE_SCORES_FROM_QUALITY=AbstractIndex.GENERATE_BASE_SCORES_FROM_QUALITY;
	final int BASE_HIT_SCORE;
	final int BASE_KEY_HIT_SCORE;
	final boolean USE_AFFINE_SCORE;
	final int EXPECTED_LEN_LIMIT;
	final int MAX_INDEL;
	
	final boolean TRIM_LIST;
	final int TIP_DELETION_SEARCH_RANGE;
	final boolean FIND_TIP_DELETIONS;
	final int ALIGN_COLUMNS_ABSTRACT;
	
	/*--------------------------------------------------------------*/
	
	
	/** Use dynamic programming slow-alignment phase to increase quality.  Program may not run anymore if this is disabled. */
	protected final boolean SLOW_ALIGN;
	/** Produce local alignments instead of global alignments */
	protected final boolean LOCAL_ALIGN;
	/** Discard reads with ambiguous alignments (consider them unmapped). */
	protected final boolean AMBIGUOUS_TOSS;
	/** Choose a random site for reads with ambiguous alignments. */
	protected final boolean AMBIGUOUS_RANDOM;
	/** Output all sites for reads with ambiguous alignments. */
	protected final boolean AMBIGUOUS_ALL;
	/** Quality-trim left side of reads before mapping. */
	protected final boolean TRIM_LEFT;
	/** Quality-trim right side of reads before mapping. */
	protected final boolean TRIM_RIGHT;
	/** Undo quality trimming after mapping. */
	protected final boolean UNTRIM;
	/** Trim until 2 consecutive bases are encountered with at least this quality. */
	protected final float TRIM_QUAL;
	protected final float TRIM_ERROR_RATE;
	/** Don't trim reads to be shorter than this */
	protected final int TRIM_MIN_LENGTH;
	/** Distance cutoff for classifying a read as loosely correct */
	protected final int THRESH;
	/** Semi-deprecated.  Minimum chrom to index or load. */
	protected final int minChrom;
	/** Semi-deprecated.  Maximum chrom to index or load. */
	protected final int maxChrom;
	/** Disallow sites that do not have at least k consecutive matching bases. */
	protected final int KFILTER;
	/** Disallow sites with identity below this. */
	protected final float IDFILTER;
	/** Do advanced filtering on number of specific types of edits */
	protected final boolean PROCESS_EDIT_FILTER;
	
	/** Rename reads to indicate their mapped insert size */
	protected final boolean RenameByInsert;
	
	/** When reads are not in valid pairing orientation, eliminate (mark unmapped) the lower-scoring read. */
	protected final boolean KILL_BAD_PAIRS;
	/** For human genome, map ambiguous reads in the PAR to the X chromosome. */
	protected final boolean SAVE_AMBIGUOUS_XY;
	/** Deprecated.  Must be set to true. */
	protected final boolean GEN_MATCH_FAST=true;
	
	/** Padding for dynamic-programming slow alignment. */
	protected final int SLOW_ALIGN_PADDING;
	/** Padding for dynamic-programming slow alignment for rescued reads (which typically may need more padding). */
	protected final int SLOW_RESCUE_PADDING;
	/** If a site is unpaired, search nearby for a possible site for the other read. */
	protected final boolean DO_RESCUE;
	/** Forbid alignments with indels longer than MAX_INDEL */
	protected final boolean STRICT_MAX_INDEL;
	/** Bandwidth of banded MSA */
	protected final int BANDWIDTH;
	
	protected final boolean PAIRED;
	protected final boolean REQUIRE_CORRECT_STRANDS_PAIRS;
	protected final boolean SAME_STRAND_PAIRS;
	
	protected final BloomFilter bloomFilter;
	
	/*--------------------------------------------------------------*/

	static int INITIAL_AVERAGE_PAIR_DIST=100;
	protected int AVERAGE_PAIR_DIST;
	protected float AVERAGE_PAIRING_RATE=0;

	/** Extra padding for when slow alignment fails. */
	protected int EXTRA_PADDING=10;
	
	protected final boolean GENERATE_KEY_SCORES_FROM_QUALITY;
	
	/*--------------------------------------------------------------*/
	
	protected static boolean PENALIZE_AMBIG=true;
	protected static int SUBFILTER=-1;
	protected static int DELFILTER=-1;
	protected static int INSFILTER=-1;
	protected static int INDELFILTER=-1;
	protected static int DELLENFILTER=-1;
	protected static int INSLENFILTER=-1;
	protected static int EDITFILTER=-1;
	protected static int NFILTER=-1;
	
	protected static boolean OUTPUT_SAM=false;
	
	protected static float SECONDARY_SITE_SCORE_RATIO=.95f;
	protected static boolean PRINT_SECONDARY_ALIGNMENTS_ONLY_FOR_AMBIGUOUS_READS=false;
	
	protected static boolean CALC_STATISTICS=true;
	protected static int MIN_PAIR_DIST=-160;
	protected static int MAX_PAIR_DIST=32000;
	protected static int MAX_RESCUE_DIST=1200;
	protected static int MAX_RESCUE_MISMATCHES=32;
	/** IMPORTANT!!!!  This option causes non-deterministic output. */
	protected static boolean DYNAMIC_INSERT_LENGTH=true;
	/** Counts undefined bases. */
	protected static final boolean DISCARD_MOSTLY_UNDEFINED_READS=true;
	protected static float MIN_AVERAGE_QUALITY=0;
	protected static int MIN_AVERAGE_QUALITY_BASES=0;
	protected static boolean TIME_TAG=false;
	protected static boolean CLEAR_ATTACHMENT=true;
	
	protected static final byte TIP_DELETION_MIN_QUALITY=6;
	protected static final byte TIP_DELETION_AVG_QUALITY=14;
	protected static final int TIP_DELETION_MAX_TIPLEN=8;
	
	protected static final int OUTER_DIST_MULT=14;
//	protected static final int OUTER_DIST_MULT2=OUTER_DIST_MULT-1;
	protected static final int OUTER_DIST_DIV=32;
	
	protected static long SKIP_INITIAL=0;
	
	protected static boolean OUTPUT_PAIRED_ONLY=false;

	protected static int MAX_READ_LENGTH=0;
	protected static int MIN_READ_LENGTH=0;
	
	protected static boolean USE_MODULO=false;
	
	protected static int MAX_TRIM_SITES_TO_RETAIN=800;
	
//	static{if(OUTER_DIST_MULT2<1){throw new RuntimeException();}}
	
	/*--------------------------------------------------------------*/
	
	public long totalNumCorrect1=0;
	public long totalNumIncorrect1=0;
	public long totalNumIncorrectPrior1=0;
	public long totalNumCapturedAllCorrect1=0;
	public long totalNumCapturedAllCorrectTop1=0;
	public long totalNumCapturedAllCorrectOnly1=0;
	
	public long totalNumCorrect2=0;
	public long totalNumIncorrect2=0;
	public long totalNumIncorrectPrior2=0;
	public long totalNumCapturedAllCorrect2=0;
	public long totalNumCapturedAllCorrectTop2=0;
	public long totalNumCapturedAllCorrectOnly2=0;
	
	/*--------------------------------------------------------------*/

	public boolean verbose=false;
	public static final boolean verboseS=false;

	public long readsUsed1=0;
	public long readsUsed2=0;
	public long basesUsed1=0;
	public long basesUsed2=0;
	public long readsIn1=0;
	public long readsIn2=0;
	public long basesIn1=0;
	public long basesIn2=0;
	public long readsPassedBloomFilter=0;
	public long basesPassedBloomFilter=0;
	public long numMated=0;
	public long numMatedBases=0;
	public long badPairs=0;
	public long badPairBases=0;
	public long innerLengthSum=0;
	public long outerLengthSum=0;
	public long insertSizeSum=0;
	public long keysUsed=0;
	public long syntheticReads=0;
	public long bothUnmapped=0;
	public long bothUnmappedBases=0;
	public long eitherMapped=0;
	public long eitherMappedBases=0;

	public long mapped1=0;
	public long mappedRetained1=0;
	public long mappedRetainedBases1=0;
	public long rescuedP1=0;
	public long rescuedM1=0;
	public long truePositiveP1=0;
	public long truePositiveM1=0;
	public long falsePositive1=0;
	public long totalCorrectSites1=0;

	public long firstSiteCorrectP1=0;
	public long firstSiteCorrectM1=0;
	public long firstSiteIncorrect1=0;
	public long firstSiteCorrectLoose1=0;
	public long firstSiteIncorrectLoose1=0;
	public long firstSiteCorrectPaired1=0;
	public long firstSiteCorrectSolo1=0;
	public long firstSiteCorrectRescued1=0;

	public long matchCountS1=0;
	public long matchCountI1=0;
	public long matchCountD1=0;
	public long matchCountM1=0;
	public long matchCountN1=0;

	public long readCountE1=0;
	public long readCountS1=0;
	public long readCountI1=0;
	public long readCountD1=0;
	public long readCountN1=0;
	public long readCountSplice1=0;
	
	public long perfectHit1=0; //Highest quick score is max quick score
	public long uniqueHit1=0; //Only one hit has highest score
	public long correctUniqueHit1=0; //unique highest hit on answer site
	public long correctMultiHit1=0;  //non-unique highest hit on answer site
	public long correctLowHit1=0;  //hit on answer site, but not highest scorer
	public long noHit1=0;
	
	/** Number of perfect hit sites found */
	public long perfectHitCount1=0;
	/** Number of sites found that are perfect except for no-ref */
	public long semiPerfectHitCount1=0;
	
	
	public long perfectMatch1=0; //Highest slow score is max slow score
	public long semiperfectMatch1=0;
	public long perfectMatchBases1=0;
	public long semiperfectMatchBases1=0;
	public long ambiguousBestAlignment1=0;
	public long ambiguousBestAlignmentBases1=0;

	public long initialSiteSum1=0;
	public long postTrimSiteSum1=0;
	public long postRescueSiteSum1=0;
	public long siteSum1=0;
	public long topSiteSum1=0;
	
	public long lowQualityReadsDiscarded1=0;
	public long lowQualityBasesDiscarded1=0;
	
	public long mapped2=0;
	public long mappedRetained2=0;
	public long mappedRetainedBases2=0;
	public long rescuedP2=0;
	public long rescuedM2=0;
	public long truePositiveP2=0;
	public long truePositiveM2=0;
	public long falsePositive2=0;
	public long totalCorrectSites2=0;

	public long firstSiteCorrectP2=0;
	public long firstSiteCorrectM2=0;
	public long firstSiteIncorrect2=0;
	public long firstSiteCorrectLoose2=0;
	public long firstSiteIncorrectLoose2=0;
	public long firstSiteCorrectPaired2=0;
	public long firstSiteCorrectSolo2=0;
	public long firstSiteCorrectRescued2=0;
	
	public long matchCountS2=0;
	public long matchCountI2=0;
	public long matchCountD2=0;
	public long matchCountM2=0;
	public long matchCountN2=0;

	public long readCountE2=0;
	public long readCountS2=0;
	public long readCountI2=0;
	public long readCountD2=0;
	public long readCountN2=0;
	public long readCountSplice2=0;
	
	public long perfectHit2=0; //Highest quick score is max quick score
	public long uniqueHit2=0; //Only one hit has highest score
	public long correctUniqueHit2=0; //unique highest hit on answer site
	public long correctMultiHit2=0;  //non-unique highest hit on answer site
	public long correctLowHit2=0;  //hit on answer site, but not highest scorer
	public long noHit2=0;
	
	/** Number of perfect hit sites found */
	public long perfectHitCount2=0;
	/** Number of sites found that are perfect except for no-ref */
	public long semiPerfectHitCount2=0;
	
	public long perfectMatch2=0; //Highest slow score is max slow score
	public long semiperfectMatch2=0;
	public long perfectMatchBases2=0;
	public long semiperfectMatchBases2=0;
	public long ambiguousBestAlignment2=0;
	public long ambiguousBestAlignmentBases2=0;

	public long initialSiteSum2=0;
	public long postTrimSiteSum2=0;
	public long postRescueSiteSum2=0;
	public long siteSum2=0;
	public long topSiteSum2=0;
	
	public long lowQualityReadsDiscarded2=0;
	public long lowQualityBasesDiscarded2=0;
	
	/*--------------------------------------------------------------*/
	
	int idmodulo;
}