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gpertea |
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#ifndef G_GAP_ASSEM_DEFINED
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#define G_GAP_ASSEM_DEFINED
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#include "GFastaFile.h"
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#include "gdna.h"
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#include "GList.hh"
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#include "GHash.hh"
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#include <ctype.h>
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class GSeqAlign;
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class MSAColumns;
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struct SeqDelOp {
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int pos;
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bool revcompl;
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SeqDelOp(int p, bool r) { pos=p; revcompl=r;}
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//
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bool operator==(SeqDelOp& d){
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return (this==&d);
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}
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bool operator>(SeqDelOp& d){
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return (this>&d);
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}
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bool operator<(SeqDelOp& d){
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return (this<&d);
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}
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};
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class GASeq : public FastaSeq {
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protected:
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int numgaps; //total number of accumulated gaps in this sequence
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short *ofs; //array of gaps at each position;
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//a negative value (-1) means DELETION of the nucleotide
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//at that position!
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#ifdef ALIGN_COVERAGE_DATA
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int* cov; //coverage of every nucleotide of this seq
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// it starts with 0 by itself
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// it'll be decreased by -1 for mismatching ends!
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#endif
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GList<SeqDelOp>* delops; //delete operations
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public:
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unsigned char flags; //8 general purpose boolean flags (bits)
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// bad_align flag is the last bit -- i.e. bit 7
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// all the others (0..6) are free for custom use
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GSeqAlign* msa;
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int msaidx; //actual index at which this sequence is to be found in GASeqAlign;
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int seqlen; // exactly the size of ofs[]
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int offset; //offset in the layout
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int ng_ofs; //non-gapped offset in the layout
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//(approx, for clipping constraints only)
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char revcompl; //0 = forward, 1=reverse
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int ext5; // layout-positional extension at 5' end
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int ext3; // layout-positional extension at 3' end
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//--
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int clp5; //ever "disproved" region at 5' end
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int clp3; //ever "disproved" region at 3' end
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//------- comparison operators (for GList) :
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//sorting by offset in cluster
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void allupper() {
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for (int i=0;i<len;i++) {
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seq[i]=toupper(seq[i]);
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}
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}
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void reverseComplement() {
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if (len==0) return;
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//ntCompTableInit();
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reverseChars(seq,len);
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for (int i=0;i<len;i++) seq[i]=ntComplement(seq[i]);
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}
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bool operator==(GASeq& d){
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return (offset==d.offset && strcmp(id,d.id)==0);
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}
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bool operator>(GASeq& d){
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return (offset>d.offset);
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}
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bool operator<(GASeq& d){
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return (offset<d.offset);
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}
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friend class GSeqAlign;
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//-------------------------------
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GASeq(char* sname, char* sdesrc=NULL, char* sseq=NULL);
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GASeq(char* sname, int soffset, int slen, int sclipL=0, int sclipR=0, char rev=0);
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~GASeq();
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void refineClipping(char* cons, int cons_len, int cpos, bool skipDels=false);
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void setGap(int pos, short gaplen=1); // set the gap in this pos
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void addGap(int pos, short gapadd); //extend the gap in this pos
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//bitno is 0 based here, for simplicity:
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inline void setFlag(unsigned char bitno) { flags |= ((unsigned char)1 << bitno); }
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inline void clearFlag(unsigned char bitno) { flags ^= ((unsigned char)1 << bitno); }
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inline bool hasFlag(unsigned char bitno) { return ( (((unsigned char)1 << bitno) & flags) !=0 ); }
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int getNumGaps() { return numgaps; }
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int gap(int pos) { return ofs[pos]; }
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void removeBase(int pos); //remove the nucleotide at that position
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int endOffset() { return offset+seqlen+numgaps; }
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int endNgOffset() { return ng_ofs+seqlen; }
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int removeClipGaps(); //remove gaps within clipped regions
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//offset should be corrected appropriately!
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void printGappedSeq(FILE* f, int baseoffs=0);
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void printGappedSeq(int baseoffs=0) { printGappedSeq(stdout, baseoffs); }
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void printGappedFasta(FILE* f);
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void loadProcessing(); //to be called immediately after loading the sequence
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// it will revCompl if needed and apply delops
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#ifdef ALIGN_COVERAGE_DATA
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void addCoverage(GASeq* s);
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#endif
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void reverseGaps(); //don't update offset and flags
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//useful after reading mgblast gap info
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void revComplement(int alignlen=0);
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void toMSA(MSAColumns& msa);
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};
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// -- nucleotide origin -- for every nucleotide in a MSA column
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// this info is needed by SNP reporting
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class NucOri {
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public:
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GASeq* seq;
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int pos; //0-based position of nucleotide letter
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NucOri() { seq=NULL; pos=0; }
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NucOri(GASeq* s, int p) { seq=s; pos=p; }
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bool operator==(NucOri& d){
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return (strcmp(seq->id,d.seq->id)==0 && pos==d.pos);
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}
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bool operator>(NucOri& d){
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int cmp=strcmp(seq->id,d.seq->id);
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if (cmp==0) return pos>d.pos;
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else return cmp>0;
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}
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bool operator<(NucOri& d){
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int cmp=strcmp(seq->id,d.seq->id);
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if (cmp==0) return pos<d.pos;
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else return cmp<0;
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}
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};
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struct SeqClipOp {
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GASeq* seq;
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int clp[2];
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SeqClipOp(GASeq* s, int newclp5, int newclp3=-1) {
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seq=s;
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clp[0]=newclp5;
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clp[1]=newclp3;
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}
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//--
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bool operator==(SeqClipOp& d){
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return (this==&d);
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}
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bool operator>(SeqClipOp& d){
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return (this>&d);
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}
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bool operator<(SeqClipOp& d){
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return (this<&d);
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}
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};
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class AlnClipOps :public GList<SeqClipOp> {
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public:
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char q_rev;
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int d5;
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int d3;
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//---
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int total;
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AlnClipOps():GList<SeqClipOp>(false,true,false) {
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total=0;
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d5=0;
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d3=0;
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q_rev=false;
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}
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bool add5(GASeq* s, int clp, float clipmax) {
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if (s->clp5<clp) {
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if (clipmax>0) {
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int maxovh = clipmax>1 ? (int)clipmax : iround(clipmax * (float)s->seqlen);
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if (clp>maxovh) return false;
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}
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//----- base test: the read should be left with no less than 25% of its length
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if (s->seqlen-s->clp3-clp < (s->seqlen >> 2)) return false;
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total+=10000+clp-s->clp5;
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Add(new SeqClipOp(s,clp,-1));
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}
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return true;
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}
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bool add3(GASeq* s, int clp, float clipmax) {
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if (s->clp3<clp) {
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if (clipmax>0) {
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int maxovh = clipmax>1 ? (int)clipmax : iround(clipmax * (float)s->seqlen);
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if (clp>maxovh) return false;
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}
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//----- base test: if the read is left with less than 25% of its length
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if (s->seqlen-s->clp5-clp < (s->seqlen >> 2)) return false;
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total+= 10000+clp-s->clp3;
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Add(new SeqClipOp(s,-1,clp));
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}
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return true;
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}
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bool add(GASeq* s, int clp5, int clp3, float clipmax) {
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int newclp5=-1;
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int newclp3=-1;
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int add=0;
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if (s->clp5<clp5) {
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if (clipmax>0) {
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int maxovh = clipmax>1 ? (int)clipmax : iround(clipmax * (float)s->seqlen);
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if (clp5>maxovh) return false;
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}
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//----- base test: if the read is left with less than 25% of its length!
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if (s->seqlen-s->clp3-clp5 < (s->seqlen >> 2)) return false;
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add+= 10000+clp5-s->clp5;
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newclp5=clp5;
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}
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else clp5=s->clp5;
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if (s->clp3<clp3) {
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if (clipmax>0) {
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int maxovh = clipmax>1 ? (int)clipmax : iround(clipmax * (float)s->seqlen);
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if (clp3>maxovh) return false;
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}
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//----- base test: if the read is left with less than 25% of its length!
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if (s->seqlen-clp5-clp3 < (s->seqlen >> 2)) return false;
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add+=10000+clp3-s->clp3;
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newclp3=clp3;
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}
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if (add>0) {
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total+=add;
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Add(new SeqClipOp(s,newclp5,newclp3));
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}
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return true;
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}
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};
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class GAlnColumn {
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protected:
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struct NucCount {
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char c; // A, C, G, T, N or -
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// precisely in this order!
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int count;
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void set(char l, int num=0) { c=l;count=num; }
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};
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enum { ncA=0, ncC, ncG, ncT, ncN, ncGap };
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NucCount counts[6];
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bool countsSorted;
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public:
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bool hasClip;
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char consensus;
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int layers; //total "thickness"
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NucOri* clipnuc;
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GList<NucOri>* nucs;
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friend int qsortnuc(const void* p1, const void* p2);
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//int total() { return numgaps+numN+numA()+numC()+numG()+numT(); }
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GAlnColumn() { //sorted?, free?, unique?
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clipnuc=NULL;
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nucs=new GList<NucOri>(false,true,false);
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/*lstC=new GList<NucOri>(false,true,false);
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lstG=new GList<NucOri>(false,true,false);
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lstT=new GList<NucOri>(false,true,false);*/
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countsSorted=false;
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counts[ncA].set('A');
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counts[ncC].set('C');
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counts[ncG].set('G');
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counts[ncT].set('T');
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counts[ncN].set('N');
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counts[ncGap].set('-');
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hasClip=false;
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layers=0;
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consensus=0;
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}
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~GAlnColumn() {
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delete nucs;
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if (clipnuc!=NULL) delete clipnuc;
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}
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void addGap() { counts[ncGap].count++;
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layers++; //-- Not a "layer", actually
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//numgaps++;
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}
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void addNuc(GASeq* seq, int pos, bool clipped=false) {
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//assumes the seq is already loaded and reverse complemented if necessary
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//position is precisely where it should be
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if (clipped) {
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if (hasClip==false) {
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hasClip=true;
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clipnuc = new NucOri(seq,pos);
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}
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return;
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}
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char c=(char)toupper(seq->seq[pos]);
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switch (c) {
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case 'A':nucs->Add(new NucOri(seq,pos));
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counts[ncA].count++;
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layers++;
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break;
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case 'C':nucs->Add(new NucOri(seq,pos));
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counts[ncC].count++;
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layers++;
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291 |
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break;
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case 'G':nucs->Add(new NucOri(seq,pos));
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counts[ncG].count++;
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layers++;
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break;
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case 'T':nucs->Add(new NucOri(seq,pos));
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counts[ncT].count++;
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layers++;
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break;
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case '-': //this shouldn't be the case!
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case '*':counts[ncGap].count++;
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layers++;
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//numgaps++;
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break;
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default: nucs->Add(new NucOri(seq,pos));
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counts[ncN].count++;
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layers++;
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//numN++;
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}//switch
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}
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312 |
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char bestChar();
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void remove(); //removes a nucleotide from all involved sequences
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//adjust all affected offsets in the alignment
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};
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317 |
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// A MSA columns container
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318 |
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class MSAColumns {
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319 |
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int size;
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320 |
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public:
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321 |
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static bool removeConsGaps;
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322 |
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static bool refineClipping;
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323 |
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GAlnColumn* columns;
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324 |
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int baseoffset;
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325 |
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int mincol;
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326 |
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int maxcol;
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327 |
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MSAColumns(int len, int baseofs=0) {
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328 |
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columns=new GAlnColumn[len];
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329 |
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size=len;
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330 |
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baseoffset=baseofs;
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331 |
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mincol=INT_MAX;
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332 |
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maxcol=0;
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333 |
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}
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334 |
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~MSAColumns() {
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335 |
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size=0;
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336 |
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baseoffset=0;
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337 |
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delete[] columns;
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338 |
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}
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339 |
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GAlnColumn& operator[](int idx) {
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340 |
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if (idx<0 || idx>=size)
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341 |
|
|
GError("MSAColumns op[]: bad index %d (size=%d)\n", idx,size);
|
342 |
|
|
return columns[idx];
|
343 |
|
|
}
|
344 |
|
|
int len() { return maxcol-mincol+1; }
|
345 |
|
|
void updateMinMax(int minc, int maxc) {
|
346 |
|
|
if (minc<mincol) mincol=minc;
|
347 |
|
|
if (maxc>maxcol) maxcol=maxc;
|
348 |
|
|
}
|
349 |
|
|
};
|
350 |
|
|
|
351 |
|
|
|
352 |
|
|
//-----------------------------------------------
|
353 |
|
|
// a sequence alignment: could be pairwise or MSA
|
354 |
|
|
class GSeqAlign :public GList<GASeq> {
|
355 |
|
|
static unsigned int counter;
|
356 |
|
|
int length;
|
357 |
|
|
int minoffset;
|
358 |
|
|
int consensus_cap;
|
359 |
|
|
void buildMSA();
|
360 |
|
|
void ErrZeroCov(int col);
|
361 |
|
|
public:
|
362 |
|
|
bool refinedMSA; //if refineMSA() was applied
|
363 |
|
|
MSAColumns* msacolumns;
|
364 |
|
|
unsigned int ordnum; //order number -- when it was created
|
365 |
|
|
// the lower the better (earlier=higher score)
|
366 |
|
|
int ng_len; //ungapped length and minoffset (approximative,
|
367 |
|
|
int ng_minofs; // for clipping constraints only)
|
368 |
|
|
int badseqs;
|
369 |
|
|
char* consensus; //consensus sequence (built by refineMSA())
|
370 |
|
|
int consensus_len;
|
371 |
|
|
friend class GASeq;
|
372 |
|
|
bool operator==(GSeqAlign& d){
|
373 |
|
|
return (this==&d);
|
374 |
|
|
}
|
375 |
|
|
bool operator>(GSeqAlign& d){
|
376 |
|
|
return (this>&d);
|
377 |
|
|
}
|
378 |
|
|
bool operator<(GSeqAlign& d){
|
379 |
|
|
return (this<&d);
|
380 |
|
|
}
|
381 |
|
|
//--
|
382 |
|
|
GSeqAlign():GList<GASeq>(true,true,false) {
|
383 |
|
|
//default is: sorted by GASeq offset, free nodes, non-unique
|
384 |
|
|
msacolumns=NULL;
|
385 |
|
|
ordnum=0;
|
386 |
|
|
length=0;
|
387 |
|
|
ng_len=0;
|
388 |
|
|
minoffset=0;
|
389 |
|
|
ng_minofs=0;
|
390 |
|
|
badseqs=0;
|
391 |
|
|
refinedMSA=false;
|
392 |
|
|
consensus=NULL;
|
393 |
|
|
consensus_len=0;
|
394 |
|
|
consensus_cap=0;
|
395 |
|
|
}
|
396 |
|
|
GSeqAlign(bool sorted, bool free_elements=true, bool beUnique=false)
|
397 |
|
|
:GList<GASeq>(sorted,free_elements,beUnique) {
|
398 |
|
|
ordnum=0;
|
399 |
|
|
length=0;
|
400 |
|
|
minoffset=0;
|
401 |
|
|
ng_len=0;
|
402 |
|
|
ng_minofs=0;
|
403 |
|
|
badseqs=0;
|
404 |
|
|
msacolumns=NULL;
|
405 |
|
|
consensus_len=0;
|
406 |
|
|
consensus_cap=0;
|
407 |
|
|
}
|
408 |
|
|
void incOrd() { ordnum = ++counter; }
|
409 |
|
|
//first time creation from a pairwise alignment:
|
410 |
|
|
#ifdef ALIGN_COVERAGE_DATA
|
411 |
|
|
GSeqAlign(GASeq* s1, int l1, int r1, GASeq* s2, int l2, int r2);
|
412 |
|
|
#else
|
413 |
|
|
GSeqAlign(GASeq* s1, GASeq* s2);
|
414 |
|
|
#endif
|
415 |
|
|
~GSeqAlign() {
|
416 |
|
|
if (msacolumns!=NULL) delete msacolumns;
|
417 |
|
|
if (consensus!=NULL) GFREE(consensus);
|
418 |
|
|
}
|
419 |
|
|
int len() { return length; }
|
420 |
|
|
|
421 |
|
|
void revComplement();
|
422 |
|
|
void addSeq(GASeq* s, int soffs, int ngofs);
|
423 |
|
|
void injectGap(GASeq* seq, int pos, int xgap);
|
424 |
|
|
void removeBase(GASeq* seq, int pos);
|
425 |
|
|
void extendConsensus(char c);
|
426 |
|
|
//try to propagate the planned trimming of a read
|
427 |
|
|
//to the whole MSA containing it
|
428 |
|
|
// returns false if too much is trimmed of any component read
|
429 |
|
|
void applyClipping(AlnClipOps& clipops);
|
430 |
|
|
|
431 |
|
|
bool evalClipping(GASeq* seq, int c5, int c3, float clipmax,
|
432 |
|
|
AlnClipOps& clipops);
|
433 |
|
|
|
434 |
|
|
//merge other alignment into this msa
|
435 |
|
|
//seq->id MUST be the same with oseq->id
|
436 |
|
|
// *if OK, gaps AND coverage values are propagated
|
437 |
|
|
// and omsa is deallocated
|
438 |
|
|
// *if not OK <=> the layout doesn't accept the merge
|
439 |
|
|
// due to clipmax constraint, then nothing happens
|
440 |
|
|
bool addAlign(GASeq* seq, GSeqAlign* omsa, GASeq* oseq);
|
441 |
|
|
void print(FILE* f, char c=0);
|
442 |
|
|
void print() { print(stdout); }
|
443 |
|
|
void removeColumn(int column);
|
444 |
|
|
void freeMSA();
|
445 |
|
|
void refineMSA(bool redo_ends=false);
|
446 |
|
|
// find consensus, refine clipping, remove gap-columns
|
447 |
|
|
void writeACE(FILE* f, const char* name);
|
448 |
|
|
void writeInfo(FILE* f, const char* name);
|
449 |
|
|
};
|
450 |
|
|
|
451 |
|
|
int compareOrdnum(void* p1, void* p2);
|
452 |
|
|
int compareCounts(void* p1, void* p2);
|
453 |
|
|
|
454 |
|
|
#endif
|