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rlink.cpp
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#include "rlink.h"
#include "GBitVec.h"
#include <float.h>
//#define GMEMTRACE 1 //debugging mem allocation
#ifdef GMEMTRACE
#include "proc_mem.h"
#endif
//import globals from main program:
//extern GffNames* gseqNames;
extern FILE *c_out; // file handle for the input transcripts that are fully covered by reads
//extern bool specific;
extern bool trim;
//extern bool partialcov;
//extern bool complete; // this is false if I use guides that are fragments, but I want them to be true
extern bool eonly;
extern bool nomulti;
extern bool fast;
//extern int maxReadCov;
extern float isofrac;
extern float mcov;
extern int mintranscriptlen; // minimum number for a transcript to be printed
//extern int sensitivitylevel;
extern uint junctionsupport; // anchor length for junction to be considered well supported <- consider shorter??
extern int junctionthr; // number of reads needed to support a particular junction
extern float readthr; // read coverage per bundle bp to accept it; otherwise considered noise
extern uint bundledist; // reads at what distance should be considered part of separate bundles
// <- this is not addressed everywhere, e.g. in infer_transcripts -> look into this
extern bool includesource;
//extern bool EM;
//extern bool weight;
extern bool geneabundance; // need to compute the gene abundance
extern float fpkm_thr;
extern float tpm_thr;
extern bool enableNames;
extern bool includecov;
extern bool retained_intron;
extern FILE* f_out;
extern GStr label;
void printTime(FILE* f) {
time_t ltime; /* calendar time */
ltime=time(NULL);
struct tm *t=localtime(<ime);
fprintf(f, "[%02d/%02d %02d:%02d:%02d]",t->tm_mon+1, t->tm_mday,
t->tm_hour, t->tm_min, t->tm_sec);
}
void printBitVec(GBitVec& bv) {
for (uint i=0;i<bv.size();i++) {
fprintf(stderr, "%c", bv.test(i)?'1':'0');
}
}
/*
CJunction* add_junction(int start, int end, int leftsupport, int rightsupport,
GList<CJunction>& junction, char strand, int nh) {
int oidx=-1;
CJunction *nj=NULL;
//CJunction* nj=junction.AddIfNew(new CJunction(start, end, strand), true, &oidx);
CJunction jn(start, end, strand);
if (junction.Found(&jn, oidx)) {
nj=junction.Get(oidx);
}
else {
nj=new CJunction(start, end, strand);
junction.Add(nj);
}
//if (nh==0) nh=1;
//nj->nreads+=float(1)/nh;
if (leftsupport >= junctionsupport && rightsupport >=junctionsupport) {
nj->nreads_good+=float(1)/nh;
}
return nj;
}
*/
CJunction* add_junction(int start, int end, GList<CJunction>& junction, char strand) {
int oidx=-1;
CJunction *nj=NULL;
//CJunction* nj=junction.AddIfNew(new CJunction(start, end, strand), true, &oidx);
CJunction jn(start, end, strand);
if (junction.Found(&jn, oidx)) {
nj=junction.Get(oidx);
}
else {
nj=new CJunction(start, end, strand);
junction.Add(nj);
}
return nj;
}
/*
void cov_add(GVec<float>& bpcov, int i, int j, float v) {
if (j>=bpcov.Count()) bpcov.Resize(j+1, 0);
for (int k=i;k<j;k++)
bpcov[k]+=v;
}
*/
void cov_add(GVec<float>* bpcov, int sno, int i, int j, float v) {
bool neutral=false;
if(sno!=1) neutral=true; // why is neutral true here: because if the sno is -/+ than I want to add their counts to bpcov[1] too
if (j>=bpcov[sno].Count())
for(int s=0;s<3;s++) bpcov[s].Resize(j+1, 0);
for (int k=i;k<=j;k++) {
bpcov[sno][k]+=v;
if(neutral) bpcov[1][k]+=v; // neutral (stranded) gets added twice here
}
}
/*
float getBCov(GVec<float>& bpcov, int p) {
//if (p<0) GMessage("Error: invalid bpcov index (%d)!\n", p);
if (p>=bpcov.Count()) return 0;
else return bpcov[p];
}
bool maxCovReached(int currentstart, GBamRecord& brec, BundleData& bdata) { // coverage saturation is reached if read spans no portion of saturation less than maxReadCov
for (int i=0;i<brec.exons.Count();i++) {
if (getBCov(bdata.bpcov, brec.exons[i].start-currentstart)<=maxReadCov)
return false;
}
if (!bdata.covSaturated) {
GMessage("Warning: bundle %s:%d-%d(%d) (%djs) reached coverage saturation (%d) starting with read mapped at %d\n",
bdata.refseq.chars(), bdata.start, bdata.end, bdata.numreads, bdata.junction.Count(),
maxReadCov, brec.start);
bdata.covSaturated=true;
}
return true;
}
*/
void countFragment(BundleData& bdata, GBamRecord& brec, int nh) {
static uint32_t BAM_R2SINGLE = BAM_FREAD2 | BAM_FMUNMAP ;
for (int i=0;i<brec.exons.Count();i++) {
bdata.frag_len+=float(1)*brec.exons[i].len()/nh;
}
if (!brec.isPaired() || ((brec.flags()&BAM_FREAD1)!=0) ||
((brec.flags()&BAM_R2SINGLE)==BAM_R2SINGLE ) ) {
bdata.num_fragments+=float(1)/nh;
}
/*
if (hi==0) {
for (int i=0;i<brec.exons.Count();i++) {
bdata.frag_len+=brec.exons[i].len();
}
if (!brec.isPaired() || ((brec.flags()&BAM_FREAD1)!=0) ||
((brec.flags()&BAM_R2SINGLE)==BAM_R2SINGLE ) ) {
bdata.num_fragments++;
}
}
else if (hi==1) {
for (int i=0;i<brec.exons.Count();i++) {
bdata.frag_len1+=brec.exons[i].len();
}
if (!brec.isPaired() || ((brec.flags()&BAM_FREAD1)!=0) ||
((brec.flags()&BAM_R2SINGLE)==BAM_R2SINGLE ) ) {
bdata.num_fragments1++;
}
}
*/
}
bool exonmatch(GVec<GSeg> &prevexons, GVec<GSeg> &exons) {
if(prevexons.Count() != exons.Count()) return false;
for(int i=0;i<exons.Count();i++) {
if(prevexons[i].end!=exons[i].end || prevexons[i].start!=exons[i].start) return false;
}
return true;
}
void processRead(int currentstart, int currentend, BundleData& bdata,
GHash<int>& hashread, GReadAlnData& alndata) { // some false positives should be eliminated here in order to break the bundle
GList<CReadAln>& readlist = bdata.readlist; // list of reads gathered so far
GList<CJunction>& junction = bdata.junction; // junctions added so far
GBamRecord& brec=*(alndata.brec); // bam record
char strand=alndata.strand;
int nh=alndata.nh;
int hi=alndata.hi;
int readstart=brec.start;
CReadAln* readaln=NULL; // readaln is initialized with NULL
//bool covSaturated=false; // coverage is set to not saturated
bool match=false; // true if current read matches a previous read
int n=readlist.Count()-1;
if(!mergeMode) while(n>-1 && readlist[n]->start==brec.start) {
if(strand==readlist[n]->strand) match=exonmatch(readlist[n]->segs,brec.exons);
if(match) break; // this way I make sure that I keep the n of the matching readlist
n--;
}
else if((alndata.tinfo->cov>=0 && alndata.tinfo->cov<readthr) || (alndata.tinfo->fpkm>=0 && alndata.tinfo->fpkm<fpkm_thr) ||
(alndata.tinfo->tpm>=0 && alndata.tinfo->tpm < tpm_thr)) return; // do not store 'read' if it doesn't meet minimum criteria
else { //mergeMode but the read is above thresholds
if(alndata.tinfo->cov>=0) bdata.covflags |= IS_COV_FLAG;
if(alndata.tinfo->fpkm>=0) bdata.covflags |= IS_FPKM_FLAG;
if(alndata.tinfo->tpm>=0) bdata.covflags |= IS_TPM_FLAG;
}
if (bdata.end<currentend) {// I am not sure why this is done here?
bdata.start=currentstart;
bdata.end=currentend;
}
bdata.numreads++; // number of reads gets increased no matter what
//bdata.wnumreads+=float(1)/nh;
if (!match) { // if this is a new read I am seeing I need to set it up
if(mergeMode && mintranscriptlen) {
int len=0;
for (int i=0;i<brec.exons.Count();i++) len+=brec.exons[i].len();
if(len<mintranscriptlen) return;
}
readaln=new CReadAln(strand, nh, brec.start, brec.end, alndata.tinfo);
alndata.tinfo=NULL; //alndata.tinfo was passed to CReadAln
for (int i=0;i<brec.exons.Count();i++) {
readaln->len+=brec.exons[i].len();
if(i) {
CJunction* nj=add_junction(brec.exons[i-1].end, brec.exons[i].start, junction, strand);
if (alndata.juncs.Count())
nj->guide_match=alndata.juncs[i-1]->guide_match;
if (nj) {
readaln->juncs.Add(nj);
}
}
readaln->segs.Add(brec.exons[i]);
}
n=readlist.Add(readaln); // reset n for the case there is no match
}
else { //redundant read alignment matching a previous alignment
// keep shortest nh so that I can see for each particular read the multi-hit proportion
if(nh<readlist[n]->nh) readlist[n]->nh=nh;
/*
//for mergeMode, we have to free the transcript info:
if (alndata.tinfo!=NULL) {
delete alndata.tinfo;
alndata.tinfo=NULL;
}
*/
}
if((int)brec.end>currentend) {
currentend=brec.end;
bdata.end=currentend;
}
float rdcount=1;
float unitig_cov=brec.tag_float("YK");
if(unitig_cov) rdcount=unitig_cov;
if(!nomulti) rdcount/=nh;
readlist[n]->read_count+=rdcount; // increase single count just in case I don't see the pair
// store the mismatch count per junction so that I can eliminate it later
int nm=brec.tag_int("NM"); // read mismatch
if(!nm) {
nm=brec.tag_int("nM"); // paired mismatch : big problem with STAR alignments
if(brec.isPaired()) nm/=2;
}
// this counts reads over allowed fraction of mismatches and multi-mapped reads
if(nh>1 || nm/readlist[n]->len>mismatchfrac) for(int i=0;i<readlist[n]->juncs.Count();i++) {
readlist[n]->juncs[i]->nm+=rdcount;
}
// now set up the pairing
if (brec.refId()==brec.mate_refId()) { //only consider mate pairing data if mates are on the same chromosome/contig and are properly paired
//if (brec.refId()==brec.mate_refId() && brec.isProperlyPaired()) { //only consider mate pairing data if mates are on the same chromosome/contig and are properly paired
//if (brec.isProperlyPaired()) { //only consider mate pairing data if mates are properly paired
int pairstart=brec.mate_start();
if (currentstart<=pairstart) { // if pairstart is in a previous bundle I don't care about it
GStr readname(brec.name());
GStr id(readname); // init id with readname
//id+=':';id+=hi; // the HI tag is not stored in all aligners, like HISAT
if(pairstart<=readstart) { // if I've seen the pair already <- I might not have seen it yet because the pair starts at the same place
id+='-';id+=pairstart;
id+=".=";id+=hi; // (!) this suffix actually speeds up the hash by improving distribution!
const int* np=hashread[id.chars()];
if(np) { // the pair was stored --> why wouldn't it be? : only in the case that the pair starts at the same position
if(readlist[*np]->nh>nh && !nomulti) rdcount=float(1)/readlist[*np]->nh;
bool notfound=true;
for(int i=0;i<readlist[*np]->pair_idx.Count();i++)
if(readlist[*np]->pair_idx[i]==n) {
readlist[*np]->pair_count[i]+=rdcount;
notfound=false;
break;
}
if(notfound) { // I didn't see the pairing before
readlist[*np]->pair_idx.Add(n);
readlist[*np]->pair_count.Add(rdcount);
}
notfound=true;
for(int i=0;i<readlist[n]->pair_idx.Count();i++)
if(readlist[n]->pair_idx[i]==*np) {
readlist[n]->pair_count[i]+=rdcount;
notfound=false;
break;
}
if(notfound) { // I didn't see the pairing before
int i=*np;
readlist[n]->pair_idx.Add(i);
readlist[n]->pair_count.Add(rdcount);
}
hashread.Remove(id.chars());
}
/* do not allow pairings starting at the same place --> way too confusing and I don't gain much info from these
else if(readstart==pairstart) { // I have not seen the pair because it starts at the same place -> need to store it
hashread.Add(id.chars(), new int(n));
}
*/
}
else { // I might still see the pair in the future
id+='-';id+=readstart; // this is the correct way
id+=".=";id+=hi;
hashread.fAdd(id.chars(), new int(n));
}
}
} //<-- if mate is mapped on the same chromosome
}
int get_min_start(CGroup **currgroup) {
int nextgr=0;
if(currgroup[0]!=NULL) {
if(currgroup[1]!=NULL) {
if(currgroup[2]!=NULL) {
int twogr = currgroup[0]->start < currgroup[1]->start ? 0 : 1;
nextgr = currgroup[twogr]->start < currgroup[2]->start ? twogr : 2;
return(nextgr);
}
else {
nextgr = currgroup[0]->start < currgroup[1]->start ? 0 : 1;
return(nextgr);
}
}
else {
if(currgroup[2]!=NULL) {
nextgr = currgroup[0]->start < currgroup[2]->start ? 0 : 2;
return(nextgr);
}
else {
return(0);
}
}
} // end if(currgroup[0]!=NULL)
else {
if(currgroup[1]!=NULL) {
if(currgroup[2]!=NULL) {
nextgr = currgroup[1]->start < currgroup[2]->start ? 1 : 2;
return(nextgr);
}
else {
return(1);
}
}
else {
return(2);
}
}
return(nextgr);
}
void set_strandcol(CGroup *prevgroup, CGroup *group, int grcol, GVec<int>& eqcol, GVec<int>& equalcolor){
int zerocol=eqcol[prevgroup->color];
if(zerocol>-1) {
while(eqcol[zerocol]!=-1 && eqcol[zerocol]!=zerocol) {
zerocol=eqcol[zerocol];
}
int tmpcol=zerocol;
while(equalcolor[zerocol]!=zerocol) {
zerocol=equalcolor[zerocol];
}
eqcol[prevgroup->color]=zerocol;
eqcol[tmpcol]=zerocol;
if(zerocol<grcol) {
equalcolor[grcol]=zerocol;
group->color=zerocol;
}
else if(grcol<zerocol) {
equalcolor[zerocol]=grcol;
eqcol[prevgroup->color]=grcol;
}
} // if(zerocol>-1)
else {
eqcol[prevgroup->color]=grcol;
}
}
void add_group_to_bundle(CGroup *group, CBundle *bundle, GPVec<CBundlenode>& bnode, uint bundledist){
CBundlenode *currlastnode=bnode[bundle->lastnodeid];
int bid=bnode.Count();
if(group->start > currlastnode->end + bundledist) { // group after last bnode
CBundlenode *currbnode=new CBundlenode(group->start,group->end,group->cov_sum,bid);
currlastnode->nextnode=currbnode;
bnode.Add(currbnode);
bundle->lastnodeid=bid;
bundle->len+=group->end-group->start+1;
bundle->cov+=group->cov_sum;
bundle->nread+=group->nread;
bundle->multi+=group->multi;
}
else { // group overlaps bnode within bundledist
if(currlastnode->end < group->end) {
bundle->len+= group->end - currlastnode->end;
currlastnode->end= group->end;
}
bundle->cov+=group->cov_sum;
bundle->nread+=group->nread;
bundle->multi+=group->multi;
currlastnode->cov+=group->cov_sum;
}
}
int create_bundle(GPVec<CBundle>& bundle,CGroup *group,GPVec<CBundlenode>& bnode) {
int bid=bnode.Count();
int bno=bundle.Count();
CBundlenode *startbnode=new CBundlenode(group->start,group->end,group->cov_sum,bid);
CBundle *newbundle=new CBundle(group->end-group->start+1,group->cov_sum,group->nread,group->multi,bid,bid);
bundle.Add(newbundle);
bnode.Add(startbnode);
return(bno);
}
int setCmp(const pointer p1, const pointer p2) {
CTrInfo *a=(CTrInfo*)p1;
CTrInfo *b=(CTrInfo*)p2;
if(a->trno<b->trno) return -1;
if(a->trno>b->trno) return 1;
return 0;
}
int capCmp(const pointer p1, const pointer p2) {
CTrInfo *a=(CTrInfo*)p1;
CTrInfo *b=(CTrInfo*)p2;
if(a->abundance<b->abundance) return -1;
if(a->abundance>b->abundance) return 1;
return 0;
}
int trCmp(const pointer p1, const pointer p2) {
CTransfrag *a=(CTransfrag*)p1;
CTransfrag *b=(CTransfrag*)p2;
if(a->nodes.Last()-a->nodes[0]<b->nodes.Last()-b->nodes[0]) return 1; // transfrag with further reach comes first
if(a->nodes.Last()-a->nodes[0]>b->nodes.Last()-b->nodes[0]) return -1;
if(a->nodes.Count()<b->nodes.Count()) return 1; // transfrag with more nodes comes first
if(a->nodes.Count()>b->nodes.Count()) return -1;
if(a->pattern.count()<b->pattern.count()) return 1;
if(a->pattern.count()>b->pattern.count()) return -1;
if(a->abundance<b->abundance) return 1;
if(a->abundance>b->abundance) return -1;
return 0;
}
int mgtrnodeCmp(const pointer p1, const pointer p2) {
CMTransfrag *a=(CMTransfrag*)p1;
CMTransfrag *b=(CMTransfrag*)p2;
if(a->transfrag->pattern.count()<b->transfrag->pattern.count()) return 1;
if(a->transfrag->pattern.count()>b->transfrag->pattern.count()) return -1;
if(!a->transfrag->real && b->transfrag->real) return -1;
if(a->transfrag->real && !b->transfrag->real) return 1;
/*if(a->transfrag->abundance<b->transfrag->abundance) return 1;
if(a->transfrag->abundance>b->transfrag->abundance) return -1;*/
return 0;
}
int mgtrabundCmp(const pointer p1, const pointer p2) {
CMTransfrag *a=(CMTransfrag*)p1;
CMTransfrag *b=(CMTransfrag*)p2;
if(!a->transfrag->real && b->transfrag->real) return 1; // guides come first
if(a->transfrag->real && !b->transfrag->real) return -1;
if(a->transfrag->abundance<b->transfrag->abundance) return 1; // most abundant transcript comes first
if(a->transfrag->abundance>b->transfrag->abundance) return -1;
if(a->transfrag->pattern.count()<b->transfrag->pattern.count()) return 1; // the one with largest pattern comes first
if(a->transfrag->pattern.count()>b->transfrag->pattern.count()) return -1;
// something to decide equal cases
if(a->transfrag->nodes.Count()<b->transfrag->nodes.Count()) return 1; // the one with most nodes comes first
if(a->transfrag->nodes.Count()>b->transfrag->nodes.Count()) return -1;
int i=0;
while(i<a->transfrag->nodes.Count()) {
if(a->transfrag->nodes[i]<b->transfrag->nodes[i]) return 1; // the transcript starting more to the left comes first
if(a->transfrag->nodes[i]>b->transfrag->nodes[i]) return -1;
i++;
}
return 0;
}
int partguideCmp(const pointer p1, const pointer p2) { // sorting partial guides in order of preference
CPartGuide *a=(CPartGuide*)p1;
CPartGuide *b=(CPartGuide*)p2;
if(a->cov<b->cov) return 1;
if(a->cov>b->cov) return -1;
if(a->gcount<b->gcount) return 1;
if(a->gcount>b->gcount) return -1;
if(a->olen<b->olen) return 1;
if(a->olen>b->olen) return -1;
if(a->allolen<b->allolen) return 1;
if(a->allolen>b->allolen) return -1;
if(a->glen<b->glen) return 1;
if(a->glen>b->glen) return -1;
return 0;
}
int edgeCmp(const pointer p1, const pointer p2) {
CNetEdge *a=(CNetEdge*)p1;
CNetEdge *b=(CNetEdge*)p2;
if(a->rate<b->rate) return 1;
if(a->rate>b->rate) return -1;
return 0;
}
int pointCmp(const pointer p1, const pointer p2) {
CTrimPoint *a=(CTrimPoint*)p1;
CTrimPoint *b=(CTrimPoint*)p2;
if(a->start && !b->start) return -1;
if(!a->start && b->start) return 1;
if(a->abundance<b->abundance) return 1;
if(a->abundance>b->abundance) return -1;
return 0;
}
int edgeCmpEM(const pointer p1, const pointer p2) {
CNetEdge *a=(CNetEdge*)p1;
CNetEdge *b=(CNetEdge*)p2;
if(a->fake && !b->fake) return 1; // check if this is right -> I want the fake one to come last
if(!a->fake && b->fake) return -1;
if(a->rate<b->rate) return 1;
if(a->rate>b->rate) return -1;
return 0;
}
int guideabundCmp(const pointer p1, const pointer p2) {
CTransfrag *a=(CTransfrag*)p1;
CTransfrag *b=(CTransfrag*)p2;
if(a->abundance<b->abundance) return 1;
if(a->abundance>b->abundance) return -1;
if(a->pattern.count()<b->pattern.count()) return 1;
if(a->pattern.count()>b->pattern.count()) return -1;
return 0;
}
int guidedabundCmp(const pointer p1, const pointer p2) {
CGuide *a=(CGuide*)p1;
CGuide *b=(CGuide*)p2;
if(a->trf->real && !b->trf->real) return 1; // this ensures included guides are treated last
if(!a->trf->real && b->trf->real) return -1;
if(a->trf->abundance<b->trf->abundance) return 1; // most abundant guide takes precedence
if(a->trf->abundance>b->trf->abundance) return -1;
if(a->trf->pattern.count()<b->trf->pattern.count()) return 1; // longest guide takes precedence
if(a->trf->pattern.count()>b->trf->pattern.count()) return -1;
return 0;
}
int guideCmp(const pointer p1, const pointer p2) {
CGuide *a=(CGuide*)p1;
CGuide *b=(CGuide*)p2;
if(a->trf->pattern.count()<b->trf->pattern.count()) return 1; // longest guide takes precedence
if(a->trf->pattern.count()>b->trf->pattern.count()) return -1;
return 0;
}
int juncCmpEnd(const pointer p1, const pointer p2) {
CJunction* a=(CJunction*)p1;
CJunction* b=(CJunction*)p2;
if (a->end<b->end) return -1;
if (a->end>b->end) return 1;
if (a->start<b->start) return -1;
if (a->start>b->start) return 1;
return 0;
}
void merge_fwd_groups(GPVec<CGroup>& group, CGroup *group1, CGroup *group2, GVec<int>& merge, GVec<int>& eqcol) {
// get end of group (group1 is assumed to come before group2)
group1->end=group2->end;
// get smallest color of group
while(eqcol[group1->color]!=group1->color) {
group1->color=eqcol[group1->color];
}
while(eqcol[group2->color]!=group2->color) {
group2->color=eqcol[group2->color];
}
if(group1->color<group2->color) {
eqcol[group2->color]=group1->color;
// print STDERR "in merge set eqcol[",$$group2[2],"]=",$$eqcol{$$group1[2]},"\n";
}
else if(group1->color>group2->color) {
eqcol[group1->color]=group2->color;
// print STDERR "in merge set eqcol[",$$group1[2],"]=",$$group2[2],"\n";
group1->color=group2->color;
}
group1->cov_sum+=group2->cov_sum;
group1->next_gr=group2->next_gr; // this is possible because group1->next_gr=group2
merge[group2->grid]=group1->grid;
group1->nread+=group2->nread;
group1->multi+=group2->multi;
// delete group2
group.freeItem(group2->grid);
}
int merge_read_to_group(int n,int np, int p, float readcov, int sno,int readcol,GList<CReadAln>& readlist,int color,GPVec<CGroup>& group,CGroup **allcurrgroup,
//CGroup **startgroup,GVec<int> *readgroup,GVec<int>& eqcol,GVec<int>& merge,float& fraglen,int *usedcol) {
CGroup **startgroup,GVec<int> *readgroup,GVec<int>& eqcol,GVec<int>& merge,int *usedcol) {
//fprintf(stderr,"merge readcol=%d\n",readcol);
CGroup *currgroup=allcurrgroup[sno];
if(currgroup != NULL) { // this type of group - negative, unknown, or positive - was created before
//set currgroup first
CGroup *lastgroup=NULL;
while(currgroup!=NULL && readlist[n]->start > currgroup->end) { // while read start after the current group's end advance group -> I might have more groups leaving from current group due to splicing
lastgroup=currgroup;
currgroup=currgroup->next_gr;
}
if(currgroup==NULL || readlist[n]->segs[0].end < currgroup->start) // currgroup is null only if we reached end of currgroup list because currgroup is not NULL initially
currgroup=lastgroup;
// now process each group of coordinates individually
CGroup *thisgroup=currgroup;
int ncoord=readlist[n]->segs.Count(); // number of "exons" in read
int lastpushedgroup=-1;
bool added=false;
for(int i=0;i<ncoord;i++) {
//fraglen+=readcov*readlist[n]->segs[i].len(); // this might be useful to have if I decide not to use the HI tag anymore
// skip groups that are left behind
while(thisgroup!=NULL && readlist[n]->segs[i].start > thisgroup->end) { // find the group where "exon" fits
lastgroup=thisgroup;
thisgroup=thisgroup->next_gr;
}
if(thisgroup && readlist[n]->segs[i].end >= thisgroup->start) { // read overlaps group
// I need to split pairs here if color didn't reach this group: it means there is a gap between these groups and no reads joining them
if(!i && np>-1 && readlist[np]->nh && np<n) { // I only consider first exon here because the rest of the groups need to get the same color
int grouppair=thisgroup->grid;
while( merge[grouppair]!=grouppair) {
grouppair=merge[grouppair];
}
thisgroup->grid=grouppair;
int thiscol=thisgroup->color;
while(eqcol[thiscol]!=thiscol) { // get smallest color
thiscol=eqcol[thiscol];
}
thisgroup->color=thiscol;
if(thiscol!=readcol) { // pair color didn't reach this group
//fprintf(stderr,"Split pairs: %d-%d and %d-%d on strand %d\n",readlist[np]->start,readlist[np]->end,readlist[n]->start,readlist[n]->end,readlist[n]->strand);
readlist[n]->pair_idx[p]=-1;
for(int j=0;j<readlist[np]->pair_idx.Count();j++)
if(readlist[np]->pair_idx[j]==n) {
readlist[np]->pair_idx[j]=-1;
break;
}
readcol=usedcol[sno]; // readcol gets back the new color
if(readcol<0) {
usedcol[sno]=color;
readcol=color;
eqcol.Add(color);
color++;
}
}
}
if(!added) { // read gets added only to first group - why ??
thisgroup->nread+=readcov;
if(readlist[n]->nh>1) thisgroup->multi+=readcov; // this will probably need to be coded differently if I do super-reads, or collapse more than one read into the same nh
added=true;
}
if(readlist[n]->segs[i].start<thisgroup->start) {
thisgroup->start=readlist[n]->segs[i].start;
}
// find end of new group
CGroup *nextgroup=thisgroup->next_gr;
while(nextgroup!=NULL && readlist[n]->segs[i].end >= nextgroup->start) {
merge_fwd_groups(group,thisgroup,nextgroup,merge,eqcol);
nextgroup=thisgroup->next_gr;
}
if(readlist[n]->segs[i].end > thisgroup->end) {
thisgroup->end=readlist[n]->segs[i].end;
}
// get smallest color of group
while(eqcol[thisgroup->color]!=thisgroup->color) {
thisgroup->color=eqcol[thisgroup->color];
}
if(readcol!=thisgroup->color) { // read color is different from group color
if(readcol<thisgroup->color) { // set group color to current read color
eqcol[thisgroup->color]=readcol;
thisgroup->color=readcol;
}
else { // read color is bigger than group
eqcol[readcol]=thisgroup->color;
readcol=thisgroup->color;
}
}
if(thisgroup->grid != lastpushedgroup) {
readgroup[n].Add(thisgroup->grid); // readgroup for read n gets the id of group
lastpushedgroup=thisgroup->grid;
}
thisgroup->cov_sum+=(readlist[n]->segs[i].end-readlist[n]->segs[i].start+1)*readcov; // coverage is different than number of reads
} // end if(thisgroup && readlist[n]->segs[i].end >= thisgroup->start)
else { // read is at the end of groups, or read is not overlapping other groups -> lastgroup is not null here because currgroup was not null
// I need to split pairs here because I have no overlap => color didn't reach here for sure if I am at the first exon
if(!i && np>-1 && readlist[np]->nh && np<n) {
//fprintf(stderr,"2 Split pairs: %d-%d and %d-%d on strand %d\n",readlist[np]->start,readlist[np]->end,readlist[n]->start,readlist[n]->end,readlist[n]->strand);
readlist[n]->pair_idx[p]=-1;
for(int j=0;j<readlist[np]->pair_idx.Count();j++)
if(readlist[np]->pair_idx[j]==n) {
readlist[np]->pair_idx[j]=-1;
break;
}
readcol=usedcol[sno]; // readcol gets back the new color
if(readcol<0) {
usedcol[sno]=color;
readcol=color;
eqcol.Add(color);
color++;
}
}
int ngroup=group.Count();
float nread=0;
float multi=0;
if(!added) {
nread=readcov;
if(readlist[n]->nh>1) multi=readcov;
added=true;
}
CGroup *newgroup=new CGroup(readlist[n]->segs[i].start,readlist[n]->segs[i].end,readcol,ngroup,(readlist[n]->segs[i].end-readlist[n]->segs[i].start+1)*readcov,nread,multi);
group.Add(newgroup);
merge.Add(ngroup);
lastgroup->next_gr=newgroup; // can lastgroup be null here -> no from the way I got here
newgroup->next_gr=thisgroup;
readgroup[n].Add(ngroup);
lastpushedgroup=ngroup;
thisgroup=lastgroup;
}
} // for(int i=0;i<ncoord;i++)
} // if(currgroup != NULL)
else { // create new group of this type
// I need to split pairs here because I have no overlap => color didn't reach here for sure
if(np>-1 && readlist[np]->nh && np<n) {
//fprintf(stderr,"3 Split pairs: %d-%d and %d-%d on strand %d\n",readlist[np]->start,readlist[np]->end,readlist[n]->start,readlist[n]->end,readlist[n]->strand);
readlist[n]->pair_idx[p]=-1;
for(int j=0;j<readlist[np]->pair_idx.Count();j++)
if(readlist[np]->pair_idx[j]==n) {
readlist[np]->pair_idx[j]=-1;
break;
}
readcol=usedcol[sno]; // readcol gets back the new color
if(readcol<0) {
usedcol[sno]=color;
readcol=color;
eqcol.Add(color);
color++;
}
}
int ncoord=readlist[n]->segs.Count();
CGroup *lastgroup=NULL;
float nread=readcov;
float multi=0;
if(readlist[n]->nh>1) multi=readcov;
for(int i=0;i<ncoord;i++) {
//fraglen+=readcov*readlist[n]->segs[i].len();
int ngroup=group.Count();
CGroup *newgroup=new CGroup(readlist[n]->segs[i].start,readlist[n]->segs[i].end,readcol,ngroup,(readlist[n]->segs[i].end-readlist[n]->segs[i].start+1)*readcov,nread,multi);
nread=0;
multi=0;
group.Add(newgroup);
merge.Add(ngroup);
if(lastgroup!=NULL) {
lastgroup->next_gr=newgroup;
}
else {
currgroup=newgroup;
}
lastgroup=newgroup;
readgroup[n].Add(ngroup);
}
}
allcurrgroup[sno]=currgroup;
if(startgroup[sno]==NULL) startgroup[sno]=currgroup;
return color;
}
int add_read_to_group(int n,GList<CReadAln>& readlist,int color,GPVec<CGroup>& group,CGroup **allcurrgroup,
//CGroup **startgroup,GVec<int> *readgroup,GVec<int>& eqcol,GVec<int>& merge,float& fraglen,uint& fragno) {
CGroup **startgroup,GVec<int> *readgroup,GVec<int>& eqcol,GVec<int>& merge) {
int usedcol[3]={-1,-1,-1};
float single_count=readlist[n]->read_count; // need to compute read single count
if(!mergeMode) for(int p=0;p<readlist[n]->pair_idx.Count();p++) {
// for each pair I have to pretend is independent of the previous one since I grouped together several reads which might be independent
int sno=readlist[n]->strand+1; // 0: negative strand; 1: zero strand; 2: positive strand (starting from -1,0,1)
// check if I've seen read's pair and if yes get its readcol; at the least get read's pair strand if available
int np=readlist[n]->pair_idx[p]; // pair read number
if(np>-1 && readlist[np]->nh) { // read pair exists and it wasn't deleted
// see if I have the correct read strand
char snop=readlist[np]->strand+1; // snop is the strand of pair read
if(sno!=snop) { // different strands for read and pair
if(sno==1) { // read n is on zero (neutral) strand, but pair has strand
// readlist[n]->strand=readlist[np]->strand; I can not update the read strand anymore -> REMEMBER this later
sno=snop; // assign strand of pair to read
}
else if(snop!=1) { // conflicting strands -> un-pair reads in the hope that one is right
readlist[n]->pair_idx[p]=-1;
for(int j=0;j<readlist[np]->pair_idx.Count();j++)
if(readlist[np]->pair_idx[j]==n) {
readlist[np]->pair_idx[j]=-1;
break;
}
np=-1;
}
}
if(np>-1) { // reads didn't get split
single_count-=readlist[n]->pair_count[p]; // update single count of read here
int readcol=usedcol[sno];
if(np<n) { // there is a pair and it came before the current read in sorted order of position
// first group of pair read is: $$readgroup[$np][0]
int grouppair=readgroup[np][0];
while( merge[grouppair]!=grouppair) {
grouppair=merge[grouppair];
}
readgroup[np][0]=grouppair;
readcol=group[readgroup[np][0]]->color; // readcol gets assigned the color of the pair's group
while(eqcol[readcol]!=readcol) { // get smallest color
readcol=eqcol[readcol];
}
//print STDERR "Adjust color of group ",$$readgroup[$np][0]," to $readcol\n";
group[readgroup[np][0]]->color=readcol;
}
else { // it's the first time I see the read in the fragment
//fragno+=readlist[n]->pair_count[p];
if(usedcol[sno]<0) { // I didn't use the color yet
usedcol[sno]=color;
readcol=color;
eqcol.Add(color); // read might keep the new color so we need to add it to the eqcol
color++;
}
}
color=merge_read_to_group(n,np,p,readlist[n]->pair_count[p],sno,readcol,readlist,color,group,
allcurrgroup,startgroup,readgroup,eqcol,merge,usedcol);
} // this ends if(np>-1)
} // if(np>-1 && readlist[np]->nh) : read pair exists and it wasn't deleted
} // for(int p=0,...)
// now I need to deal with the single count
if(mergeMode || single_count>epsilon) { // my way of controlling for rounding errors
//fragno+=single_count;
int readcol=usedcol[readlist[n]->strand+1];
if(readcol<0) {
readcol=color;
usedcol[readlist[n]->strand+1]=color;
eqcol.Add(color); // read might keep the new color so we need to add it to the eqcol
color++;
}
color=merge_read_to_group(n,-1,-1,single_count,readlist[n]->strand+1,readcol,readlist,color,group,
allcurrgroup,startgroup,readgroup,eqcol,merge,usedcol);
}
return color;
}
CGraphnode *create_graphnode(int s, int g, uint start,uint end,int nodeno,CBundlenode *bundlenode,
GVec<CGraphinfo> **bundle2graph,GPVec<CGraphnode> **no2gnode) {
/*
{ // DEBUG ONLY
fprintf(stderr,"create_graphnode[%d][%d]:%d-%d\n",s,g,start,end);
}
*/
CGraphnode* gnode=new CGraphnode(start,end,nodeno);
CGraphinfo ginfo(g,nodeno);
bundle2graph[s][bundlenode->bid].Add(ginfo);
no2gnode[s][g].Add(gnode);
return(gnode);
}
float compute_chi(GArray<float>& winleft, GArray<float>& winright, float sumleft, float sumright) {
float chi=0;
for(int j=0;j<CHI_WIN;j++) {
float mul=(winleft[j]+ winright[j])/(sumleft+sumright);
float mur=mul;
mul*=sumleft;
mur*=sumright;
// I wasn't squaring before but it doesn't make sense not to because then I would add a bunch of negatives
if(mul) chi+= (winleft[j]-mul)*(winleft[j]-mul)/mul;
if(mur) chi+=(winright[j]-mur)*(winright[j]-mur)/mur;
}
return(chi);
}
float compute_chi2(GArray<float>& winleft, GArray<float>& winright, float sumleft, float sumright) {
float chi=0;
float basecost=0;
float leftcost=0;
float rightcost=0;
float mubase=(sumleft+sumright)/(2*CHI_WIN);
float muleft=sumleft/CHI_WIN;
float muright=sumright/CHI_WIN;
for(int j=0;j<CHI_WIN;j++) {
basecost+=(winleft[j]-mubase)*(winleft[j]-mubase)+(winright[j]-mubase)*(winright[j]-mubase);
leftcost+=(winleft[j]-muleft)*(winleft[j]-muleft);
rightcost+=(winright[j]-muright)*(winright[j]-muright);
}
chi=basecost/(2*CHI_WIN)-(leftcost+rightcost)/CHI_WIN;
return(chi);
}