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package structures;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.concurrent.atomic.AtomicLong;
import dna.AminoAcid;
import fileIO.FileFormat;
import ml.CellNet;
import ml.ScoreSequence;
import shared.Parse;
import shared.Tools;
import stream.FastaReadInputStream;
import stream.Read;
public class SeqMap extends LongArrayListHashMap<SeqPos> {
public SeqMap(){this(11,1,0);}
public SeqMap(int k_, int maskMiddle_, int minCount_){
super();
k=k_;
maskMiddle=maskMiddle_;
minCount=minCount_;
long mask=0;
if(maskMiddle>0){
assert(k>maskMiddle+1);
int bits=maskMiddle*2;
int shift=(k-maskMiddle)&(~1);//Equivalent to (x/2)*2
mask=~((-1L)<<bits);
mask<<=(shift);
}
midMask=mask;
}
public void add(byte[] s, int count, final float score) {
if(s==null || s.length<k){return;}
final int shift=2*k;
final long mask=(shift>63 ? -1L : ~((-1L)<<shift));
long kmer=0;
int len=0;
final int code=Tools.hash(s, 22);
final float gc=Tools.calcGC(s);
/* Loop through s, maintaining a forward kmer via bitshifts */
for(int i=0; i<s.length; i++){
byte b=s[i];
long x=symbolToNumber[b];
kmer=((kmer<<2)|x)&mask;
if(x<0){
len=0;
}else{len++;}
if(len>=k){
long mmKmer=kmer|midMask;
SeqPos sp=new SeqPos(s, i, count, code, gc, score);
put(mmKmer, sp);
}
}
}
public ArrayList<SeqPosM> fetch(byte[] query, final int a1, final int b1, final int minOverlap0, int maxMM,
final int maxTrim, final int maxLopsidedness, float minOverlapFractionQ, boolean sort){
final float qgc=Tools.calcGC(query, a1, b1);
final int qlen=b1-a1+1;
if(query==null || query.length<k || qlen<k){return null;}
queries.incrementAndGet();
final int minOverlapQ=Tools.max(minOverlap0, (int)(minOverlapFractionQ*qlen));
final int shift=2*k;
final long mask=(shift>63 ? -1L : ~((-1L)<<shift));
long kmer=0;
int len=0;
long lookups=0;
HashSet<SeqPosM> set=localSet.get();
ArrayList<SeqPosM> retList=localList.get();
SeqPosM temp=localSP.get();
assert(set.isEmpty());
retList.clear();
final float maxGCO=Tools.max(2.8f, maxMM+0.5f); //gcdif*overlap, proxy for mismatches
/* Loop through s, maintaining a forward kmer via bitshifts */
for(int i=a1; i<=b1; i++){
// System.err.println("i="+i);
byte b=query[i];
long x=symbolToNumber[b];
kmer=((kmer<<2)|x)&mask;
if(x<0){
len=0;
}else{len++;}
if(len>=k){
long mmKmer=kmer|midMask;
ArrayList<SeqPos> candidates=get(mmKmer);
// if(candidates!=null) {
// for(SeqPos sp : candidates) {
// final float gcdif=Tools.absdif(qgc, sp.gc);
//// if(Tools.absdif(qgc, sp.gc)<0.24f) {//Intended to increase speed, but not very useful
// final int rlen0=sp.seq().length, pos=sp.pos();
// int a2=i-pos;
// int b2=Tools.min(query.length-1, a2+rlen0-1);
// a2=Tools.max(0, a2);
//// final int rlen=b2-a2+1;
// final int overlap=Range.overlap(a1, b1, a2, b2);
// final int lopsidedness=Range.lopsidedness(a1, b1, a2, b2);
//// final int minOverlapR=Tools.max(minOverlap0, (int)(minOverlapFractionR*rlen));
// final int trim=Tools.max(a2-a1, b1-b2);
//// System.err.println("rlen="+rlen+", minOverlapR="+minOverlapR+", overlap="+overlap+", "+
//// new String(query, a2, rlen));
//// System.err.println("("+a1+"-"+b1+", "+a2+"-"+b2);
//
// if(overlap>=minOverlapQ && trim<=maxTrim && lopsidedness<=maxLopsidedness
// && (gcdif*overlap<maxGCO)) {
//// assert(a2<=a1 && b2>=b1) : a1+"-"+b1+", "+a2+"-"+b2+"; trim="+trim+"; max="+maxTrim;
// temp.setFrom(sp);
// temp.setPos(i-pos);
// lookups++;
// if(!set.contains(temp)) {
// SeqPosM clone=temp.clone();
// set.add(clone);
// retList.add(clone);
// }
//// assert(a1==a2 && b1==b2) : "("+a1+"-"+b1+", "+a2+"-"+b2+"), "+
//// overlap+", "+minOverlapQ+", "+minOverlapR;
// }
//// }
// }
// }
if(candidates!=null) {//More concise. Probably same speed.
lookups+=addCandidates(candidates, query, a1, b1, qgc,
minOverlapQ, maxTrim, maxLopsidedness, maxGCO, i, temp, set, retList);
}
}
}
// ArrayList<SeqPosM> retList=null;
if(!set.isEmpty()) {
assert(set.size()==retList.size());
// list=new ArrayList<SeqPosM>(set.size());
// list.addAll(set);
if(sort) {Collections.sort(retList);}
}else {retList=null;}
set.clear();
// temp.seq=null;
setQueries.addAndGet(lookups);
return retList;
}
public ArrayList<SeqPosM> doubleFetch(byte[] query, final int a1, final int b1, final int a2, final int b2,
final int minOverlap0, int maxMM,
final int maxTrim, final int maxLopsidedness, float minOverlapFractionQ, boolean sort){
final float qgc=Tools.calcGC(query, a1, b1);
final float qgc2=Tools.calcGC(query, a2, b2);
final int qlen=b1-a1+1;
assert(qlen==b2-a2+1);
if(query==null || query.length<k || qlen<k){return null;}
queries.incrementAndGet();
final int minOverlapQ=Tools.max(minOverlap0, (int)(minOverlapFractionQ*qlen));
final int shift=2*k;
final long mask=(shift>63 ? -1L : ~((-1L)<<shift));
long kmer=0, kmer2=0;
int len=0, len2=0;
long lookups=0;
HashSet<SeqPosM> set=localSet.get();
ArrayList<SeqPosM> retList=localList.get();
SeqPosM temp=localSP.get();
assert(set.isEmpty());
retList.clear();
final float maxGCO=Tools.max(2.8f, maxMM+0.5f); //gcdif*overlap, proxy for mismatches
/* Loop through s, maintaining a forward kmer via bitshifts */
for(int i=a1, j=a2; i<=b1; i++, j++){
// System.err.println("i="+i);
byte b=query[i], c=query[j];
long x=symbolToNumber[b], y=symbolToNumber[c];
kmer=((kmer<<2)|x)&mask;
kmer2=((kmer2<<2)|y)&mask;
if(x<0){len=0;}else{len++;}
if(y<0){len2=0;}else{len2++;}
final long mmKmer=kmer|midMask, mmKmer2=kmer2|midMask;
if(len>=k){
ArrayList<SeqPos> candidates=get(mmKmer);
if(candidates!=null) {
lookups+=addCandidates(candidates, query, a1, b1, qgc,
minOverlapQ, maxTrim, maxLopsidedness, maxGCO, i, temp, set, retList);
}
}
if(len2>=k && mmKmer!=mmKmer2){
ArrayList<SeqPos> candidates=get(mmKmer2);
if(candidates!=null) {//This a1 and b1 is intentional, to keep pos left-relative
lookups+=addCandidates(candidates, query, a1, b1, qgc2,
minOverlapQ, maxTrim, maxLopsidedness, maxGCO, i, temp, set, retList);
}
}
}
// ArrayList<SeqPosM> retList=null;
if(!set.isEmpty()) {
assert(set.size()==retList.size());
// list=new ArrayList<SeqPosM>(set.size());
// list.addAll(set);
if(sort) {Collections.sort(retList);}
}else {retList=null;}
set.clear();
// temp.seq=null;
setQueries.addAndGet(lookups);
return retList;
}
private int addCandidates(ArrayList<SeqPos> candidates, byte[] query, final int a1, final int b1, float qgc,
int minOverlapQ, int maxTrim, int maxLopsidedness, float maxGCO, int qpos,
SeqPosM temp, HashSet<SeqPosM> set, ArrayList<SeqPosM> retList) {
int lookups=0;
for(SeqPos sp : candidates) {
final float gcdif=Tools.absdif(qgc, sp.gc);
final int rlen0=sp.seq().length, pos=sp.pos();
int a3=qpos-pos;
int b3=Tools.min(query.length-1, a3+rlen0-1);
a3=Tools.max(0, a3);
final int overlap=Range.overlap(a1, b1, a3, b3);
final int lopsidedness=Range.lopsidedness(a1, b1, a3, b3);
final int trim=Tools.max(a3-a1, b1-b3);
if(overlap>=minOverlapQ && trim<=maxTrim && lopsidedness<=maxLopsidedness
&& (gcdif*overlap<maxGCO)) {
temp.setFrom(sp);
temp.setPos(qpos-pos);
lookups++;
if(!set.contains(temp)) {
SeqPosM clone=temp.clone();
set.add(clone);
retList.add(clone);
}
}
}
return lookups;
}
public int sort() {
int max=0;
for(ArrayList<SeqPos> list : values()) {
if(list!=null && !list.isEmpty()) {
Collections.sort(list);
max=Tools.max(max, list.get(0).count);
}
// assert(false) : max;
}
return max;
}
public static SeqMap load(String ref, int k, int mm, int minCount, boolean rcomp, CellNet net) {
ArrayList<Read> reads=FastaReadInputStream.toReads(ref, FileFormat.FASTA, -1);
return load(reads, k, mm, minCount, rcomp, net);
}
public static SeqMap load(ArrayList<Read> reads, int k, int mm, int minCount, boolean rcomp, CellNet net) {
SeqMap map=new SeqMap(k, mm, minCount);
int maxCount=0;
float[] vec=(net==null ? null : new float[net.numInputs()]);
synchronized(map) {
for(Read r : reads) {
String id=r.id;
int x=id.indexOf("count=");
int count=(x>=0 ? Parse.parseInt(id, x+6) : 1);
int y=id.indexOf("score=");
float score=(y>=0 ? Parse.parseFloat(id, y+6) : -1);
if((y<0 || score==-1) && net!=null) {
score=ScoreSequence.score(r.bases, vec, 0, net);
}
maxCount=Tools.max(count, maxCount);
if(x<0 || count>=minCount) {
map.add(r.bases, count, score);
if(rcomp) {map.add(AminoAcid.reverseComplementBases(r.bases), count, score);}
}
}
}
assert(maxCount>=minCount) : "Error: minRefCount="+minCount+
" was set too high for the reference, whose highest count was "+maxCount+
"\nOnly set minRefCount if your ref headers have a 'count=X' term.";
return map;
}
public final int k;
public final int maskMiddle;
public final int minCount;
private final long midMask;
private static final byte[] symbolToNumber=AminoAcid.baseToNumber;
private final ThreadLocal<HashSet<SeqPosM>> localSet=new ThreadLocal<HashSet<SeqPosM>>(){
@Override protected HashSet<SeqPosM> initialValue() {return new HashSet<SeqPosM>();}
};
private final ThreadLocal<ArrayList<SeqPosM>> localList=new ThreadLocal<ArrayList<SeqPosM>>(){
@Override protected ArrayList<SeqPosM> initialValue() {return new ArrayList<SeqPosM>();}
};
private final ThreadLocal<SeqPosM> localSP=new ThreadLocal<SeqPosM>(){
@Override protected SeqPosM initialValue() {return new SeqPosM(null, 0);}
};
public final AtomicLong queries=new AtomicLong(0);
public final AtomicLong setQueries=new AtomicLong(0);
}
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