void cluster_mRNAs(GList<GffObj> & mrnas, GList<GLocus> & loci, int qfidx) {
//mrnas sorted by start coordinate
//and so are the loci
//int rdisc=0;
for (int t=0;t<mrnas.Count();t++) {
GArray<int> mrgloci(false);
GffObj* mrna=mrnas[t];
int lfound=0; //count of parent loci
/*for (int l=0;l<loci.Count();l++) {
if (loci[l]->end<mrna->exons.First()->start) continue;
if (loci[l]->start>mrna->exons.Last()->end) break; */
for (int l=loci.Count()-1;l>=0;l--) {
if (loci[l]->end<mrna->exons.First()->start) {
if (mrna->exons.First()->start-loci[l]->start > GFF_MAX_LOCUS) break;
continue;
}
if (loci[l]->start>mrna->exons.Last()->end) continue;
//here we have mrna overlapping loci[l]
if (loci[l]->add_mRNA(mrna)) {
//a parent locus was found
lfound++;
mrgloci.Add(l); //locus indices added here, in decreasing order
}
}//loci loop
//if (lfound<0) continue; //mrna was a ref duplicate, skip it
if (lfound==0) {
//create a locus with only this mRNA
loci.Add(new GLocus(mrna, qfidx));
}
else if (lfound>1) {
//more than one locus found parenting this mRNA, merge loci
lfound--;
for (int l=0;l<lfound;l++) {
int mlidx=mrgloci[l]; //largest indices first, so it's safe to remove
loci[mrgloci[lfound]]->addMerge(*loci[mlidx], mrna);
loci.Delete(mlidx);
}
}
}//mrnas loop
//if (rdisc>0) mrnas.Pack();
//return rdisc;
}
bool GffLoader::placeGf(GffObj* t, GenomicSeqData* gdata, bool doCluster, bool collapseRedundant,
bool matchAllIntrons, bool fuzzSpan) {
bool keep=false;
GTData* tdata=NULL;
//int tidx=-1;
/*
if (debug) {
GMessage(">>Placing transcript %s\n", t->getID());
debugState=true;
}
else debugState=false;
*/
//dumb TRNA case for RefSeq: gene parent link missing
//try to restore it here; BUT this only works if gene feature comes first
////DEBUG ONLY:
//if (strcmp(t->getID(),"id24448")==0) { //&& t->start==309180) {
// GMessage("placeGf %s (%d, %d) (%d exons)\n", t->getID(),t->start, t->end, t->exons.Count());
//}
//GMessage("DBG>>Placing transcript %s(%d-%d, %d exons)\n", t->getID(), t->start, t->end, t->exons.Count());
if (t->parent==NULL && t->isTranscript()) {
int gidx=gdata->gfs.Count()-1;
while (gidx>=0 && gdata->gfs[gidx]->end>=t->start) {
GffObj& g = *(gdata->gfs[gidx]);
if (g.isGene() && t->strand==g.strand && exonOverlap2Gene(t, g)) {
g.children.Add(t);
keep=true;
if (tdata==NULL) {
tdata=new GTData(t); //additional transcript data
gdata->tdata.Add(tdata);
}
t->parent=&g;
//disable printing of gene if transcriptsOnly
if (transcriptsOnly) {
g.udata|=4; //tag it as non-printable
}
const char* geneName=g.getAttr("Name");
if (t->getAttr("Name")==NULL && geneName) {
t->addAttr("Name", geneName);
t->addAttr("gene_name", geneName);
}
t->addAttr("geneID", g.getID());
break;
}
--gidx;
}
}
/*
if (t->exons.Count()==0 && t->children.Count()==0 && forceExons) {
//a non-mRNA feature with no subfeatures
//just so we get some sequence functions working, add a dummy "exon"-like subfeature here
//--this could be a single "pseudogene" entry or another genomic region without exons
//
t->addExon(t->start,t->end);
}
*/
if (t->exons.Count()>0) {
gdata->rnas.Add(t); //added it in sorted order
if (tdata==NULL) {
tdata=new GTData(t); //additional transcript data
gdata->tdata.Add(tdata);
}
keep=true;
}
else {
if (t->isGene() || !this->transcriptsOnly) {
gdata->gfs.Add(t);
keep=true;
//GTData* tdata=new GTData(t); //additional transcript data
if (tdata==NULL) {
tdata=new GTData(t); //additional transcript data
gdata->tdata.Add(tdata);
}
return true;
}
else
return false; //nothing to do with these non-transcript objects
}
if (!doCluster) return keep;
if (!keep) return false;
//---- place into a locus
if (gdata->loci.Count()==0) {
gdata->loci.Add(new GffLocus(t));
return true; //new locus on this ref seq
}
int nidx=qsearch_gloci(t->end, gdata->loci); //get index of nearest locus starting just ABOVE t->end
//GMessage("\tlooking up end coord %d in gdata->loci.. (qsearch got nidx=%d)\n", t->end, nidx);
if (nidx==0) {
//cannot have any overlapping loci
//if (debug) GMessage(" <<no ovls possible, create locus %d-%d \n",t->start, t->end);
gdata->loci.Add(new GffLocus(t));
return true;
}
if (nidx==-1) nidx=gdata->loci.Count();//all loci start below t->end
int lfound=0; //count of parent loci
GArray<int> mrgloci(false);
GList<GffLocus> tloci(true); //candidate parent loci to adopt this
//if (debug) GMessage("\tchecking all loci from %d to 0\n",nidx-1);
for (int l=nidx-1;l>=0;l--) {
GffLocus& loc=*(gdata->loci[l]);
if (loc.strand!='.' && t->strand!='.'&& loc.strand!=t->strand) continue;
if (t->start>loc.end) {
if (t->start-loc.start>GFF_MAX_LOCUS) break; //give up already
continue;
}
if (loc.start>t->end) {
//this should never be the case if nidx was found correctly
GMessage("Warning: qsearch_gloci found loc.start>t.end!(t=%s)\n", t->getID());
continue;
}
if (loc.add_RNA(t)) {
//will add this transcript to loc
lfound++;
mrgloci.Add(l);
if (collapseRedundant) {
//compare to every single transcript in this locus
for (int ti=0;ti<loc.rnas.Count();ti++) {
if (loc.rnas[ti]==t) continue;
GTData* odata=(GTData*)(loc.rnas[ti]->uptr);
//GMessage(" ..redundant check vs overlapping transcript %s\n",loc.rnas[ti]->getID());
GffObj* container=NULL;
if (odata->replaced_by==NULL &&
(container=redundantTranscripts(*t, *(loc.rnas[ti]), matchAllIntrons, fuzzSpan))!=NULL) {
if (container==t) {
odata->replaced_by=t;
preserveContainedCDS(t, loc.rnas[ti]);
}
else {// t is being replaced by previously defined transcript
tdata->replaced_by=loc.rnas[ti];
preserveContainedCDS(loc.rnas[ti], t);
}
}
}//for each transcript in the exon-overlapping locus
} //if doCollapseRedundant
} //overlapping locus
} //for each existing locus
if (lfound==0) {
//overlapping loci not found, create a locus with only this mRNA
int addidx=gdata->loci.Add(new GffLocus(t));
if (addidx<0) {
//should never be the case!
GMessage(" WARNING: new GffLocus(%s:%d-%d) not added!\n",t->getID(), t->start, t->end);
}
}
else { //found at least one overlapping locus
lfound--;
int locidx=mrgloci[lfound];
GffLocus& loc=*(gdata->loci[locidx]);
//last locus index found is also the smallest index
if (lfound>0) {
//more than one loci found parenting this mRNA, merge loci
/* if (debug)
GMessage(" merging %d loci \n",lfound);
*/
for (int l=0;l<lfound;l++) {
int mlidx=mrgloci[l];
loc.addMerge(*(gdata->loci[mlidx]), t);
gdata->loci.Delete(mlidx); //highest indices first, so it's safe to remove
}
}
int i=locidx;
while (i>0 && loc<*(gdata->loci[i-1])) {
//bubble down until it's in the proper order
i--;
gdata->loci.Swap(i,i+1);
}
}//found at least one overlapping locus
return true;
}
