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gff_utils.cpp
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gff_utils.cpp
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#include "gff_utils.h"
extern bool verbose;
//extern bool debugMode;
//bool debugState=false;
void printFasta(FILE* f, GStr& defline, char* seq, int seqlen) {
if (seq==NULL) return;
int len=(seqlen>0)?seqlen:strlen(seq);
if (len<=0) return;
if (!defline.is_empty())
fprintf(f, ">%s\n",defline.chars());
int ilen=0;
for (int i=0; i < len; i++, ilen++) {
if (ilen == 70) {
fputc('\n', f);
ilen = 0;
}
putc(seq[i], f);
} //for
fputc('\n', f);
}
int qsearch_gloci(uint x, GList<GffLocus>& loci) {
//binary search
//do the simplest tests first:
if (loci[0]->start>x) return 0;
if (loci.Last()->start<x) return -1;
uint istart=0;
int i=0;
int idx=-1;
int maxh=loci.Count()-1;
int l=0;
int h = maxh;
while (l <= h) {
i = (l+h)>>1;
istart=loci[i]->start;
if (istart < x) l = i + 1;
else {
if (istart == x) { //found matching coordinate here
idx=i;
while (idx<=maxh && loci[idx]->start==x) {
idx++;
}
return (idx>maxh) ? -1 : idx;
}
h = i - 1;
}
} //while
idx = l;
while (idx<=maxh && loci[idx]->start<=x) {
idx++;
}
return (idx>maxh) ? -1 : idx;
}
int qsearch_rnas(uint x, GList<GffObj>& rnas) {
//binary search
//do the simplest tests first:
if (rnas[0]->start>x) return 0;
if (rnas.Last()->start<x) return -1;
uint istart=0;
int i=0;
int idx=-1;
int maxh=rnas.Count()-1;
int l=0;
int h = maxh;
while (l <= h) {
i = (l+h)>>1;
istart=rnas[i]->start;
if (istart < x) l = i + 1;
else {
if (istart == x) { //found matching coordinate here
idx=i;
while (idx<=maxh && rnas[idx]->start==x) {
idx++;
}
return (idx>maxh) ? -1 : idx;
}
h = i - 1;
}
} //while
idx = l;
while (idx<=maxh && rnas[idx]->start<=x) {
idx++;
}
return (idx>maxh) ? -1 : idx;
}
int cmpRedundant(GffObj& a, GffObj& b) {
if (a.exons.Count()==b.exons.Count()) {
if (a.covlen==b.covlen) {
return strcmp(a.getID(), b.getID());
}
else return (a.covlen>b.covlen)? 1 : -1;
}
else return (a.exons.Count()>b.exons.Count())? 1: -1;
}
bool tMatch(GffObj& a, GffObj& b) {
//strict intron chain match, or single-exon perfect match
int imax=a.exons.Count()-1;
int jmax=b.exons.Count()-1;
int ovlen=0;
if (imax!=jmax) return false; //different number of introns
if (imax==0) { //single-exon mRNAs
//if (equnspl) {
//fuzz match for single-exon transfrags:
// it's a match if they overlap at least 80% of max len
ovlen=a.exons[0]->overlapLen(b.exons[0]);
int maxlen=GMAX(a.covlen,b.covlen);
return (ovlen>=maxlen*0.8);
/*}
else {
//only exact match
ovlen=a.covlen;
return (a.exons[0]->start==b.exons[0]->start &&
a.exons[0]->end==b.exons[0]->end);
}*/
}
//check intron overlaps
ovlen=a.exons[0]->end-(GMAX(a.start,b.start))+1;
ovlen+=(GMIN(a.end,b.end))-a.exons.Last()->start;
for (int i=1;i<=imax;i++) {
if (i<imax) ovlen+=a.exons[i]->len();
if ((a.exons[i-1]->end!=b.exons[i-1]->end) ||
(a.exons[i]->start!=b.exons[i]->start)) {
return false; //intron mismatch
}
}
return true;
}
bool unsplContained(GffObj& ti, GffObj& tj, bool fuzzSpan) {
//returns true only if ti (which MUST be single-exon) is "almost" contained in any of tj's exons
//but it does not cross any intron-exon boundary of tj
int imax=ti.exons.Count()-1;
int jmax=tj.exons.Count()-1;
if (imax>0) GError("Error: bad unsplContained() call, 1st param must be single-exon transcript!\n");
int minovl = (int)(0.8 * ti.len()); //minimum overlap for fuzzSpan
if (fuzzSpan) {
for (int j=0;j<=jmax;j++) {
//must NOT overlap the introns
if ((j>0 && ti.start<tj.exons[j]->start)
|| (j<jmax && ti.end>tj.exons[j]->end))
return false;
if (ti.exons[0]->overlapLen(tj.exons[j])>=minovl)
return true;
}
} else {
for (int j=0;j<=jmax;j++) {
//must NOT overlap the introns
if ((j>0 && ti.start<tj.exons[j]->start)
|| (j<jmax && ti.end>tj.exons[j]->end))
return false;
//strict containment
if (ti.end<=tj.exons[j]->end && ti.start>=tj.exons[j]->start)
return true;
}
}
return false;
}
GffObj* redundantTranscripts(GffObj& ti, GffObj& tj, bool matchAllIntrons, bool fuzzSpan) {
// matchAllIntrons==true: transcripts are considered "redundant" only if
// they have the exact same number of introns and same splice sites (or none)
// (single-exon transcripts can be also fully contained to be considered matching)
// matchAllIntrons==false: an intron chain could be a subset of a "container" chain,
// as long as no intron-exon boundaries are violated; also, a single-exon
// transcript will be collapsed if it's contained in one of the exons of the other
// fuzzSpan==false: the genomic span of one transcript must be contained in or equal with the genomic
// span of the other
//
// fuzzSpan==true: then genomic spans of transcripts are no longer required to be fully contained
// (i.e. they may extend each-other in opposite directions)
//if redundancy is detected, the "bigger" transcript is returned (otherwise NULL is returned)
if (ti.start>=tj.end || tj.start>=ti.end || tj.strand!=ti.strand) return NULL; //no span overlap at all
int imax=ti.exons.Count()-1;
int jmax=tj.exons.Count()-1;
GffObj* bigger=NULL;
GffObj* smaller=NULL;
if (matchAllIntrons) {
if (imax!=jmax) return NULL;
if (ti.covlen>tj.covlen) {
bigger=&ti;
if (!fuzzSpan && (ti.start>tj.start || ti.end<tj.end)) return NULL;
}
else { //ti.covlen<=tj.covlen
bigger=&tj;
if (!fuzzSpan && (tj.start>ti.start || tj.end<ti.end)) return NULL;
}
//check that all introns really match
for (int i=0;i<imax;i++) {
if (ti.exons[i]->end!=tj.exons[i]->end ||
ti.exons[i+1]->start!=tj.exons[i+1]->start) return NULL;
}
return bigger;
}
//--- matchAllIntrons==false: intron-chain containment is also considered redundancy
//int maxlen=0;
int minlen=0;
if (ti.covlen>tj.covlen) {
if (tj.exons.Count()>ti.exons.Count()) {
//exon count override
bigger=&tj;
smaller=&ti;
}
else {
bigger=&ti;
smaller=&tj;
}
//maxlen=ti.covlen;
minlen=tj.covlen;
}
else { //tj has more bases
if (ti.exons.Count()>tj.exons.Count()) {
//exon count override
bigger=&ti;
smaller=&tj;
}
else {
bigger=&tj;
smaller=&ti;
}
//maxlen=tj.covlen;
minlen=ti.covlen;
}
if (imax==0 && jmax==0) {
//single-exon transcripts: if fuzzSpan, at least 80% of the shortest one must be overlapped by the other
if (fuzzSpan) {
return (ti.exons[0]->overlapLen(tj.exons[0])>=minlen*0.8) ? bigger : NULL;
}
else {
return (smaller->start>=bigger->start && smaller->end<=bigger->end) ? bigger : NULL;
}
}
//containment is also considered redundancy
if (smaller->exons.Count()==1) {
//check if this single exon is contained in any of tj exons
//without violating any intron-exon boundaries
return (unsplContained(*smaller, *bigger, fuzzSpan) ? bigger : NULL);
}
//--from here on: both are multi-exon transcripts, imax>0 && jmax>0
if (ti.exons[imax]->start<tj.exons[0]->end ||
tj.exons[jmax]->start<ti.exons[0]->end )
return NULL; //intron chains do not overlap at all
//checking full intron chain containment
uint eistart=0, eiend=0, ejstart=0, ejend=0; //exon boundaries
int i=1; //exon idx to the right of the current intron of ti
int j=1; //exon idx to the right of the current intron of tj
//find the first intron overlap:
while (i<=imax && j<=jmax) {
eistart=ti.exons[i-1]->end;
eiend=ti.exons[i]->start;
ejstart=tj.exons[j-1]->end;
ejend=tj.exons[j]->start;
if (ejend<eistart) { j++; continue; }
if (eiend<ejstart) { i++; continue; }
//we found an intron overlap
break;
}
if (!fuzzSpan && (bigger->start>smaller->start || bigger->end < smaller->end)) return NULL;
if ((i>1 && j>1) || i>imax || j>jmax) {
return NULL; //either no intron overlaps found at all
//or it's not the first intron for at least one of the transcripts
}
if (eistart!=ejstart || eiend!=ejend) return NULL; //not an exact intron match
if (j>i) {
//i==1, ti's start must not conflict with the previous intron of tj
if (ti.start<tj.exons[j-1]->start) return NULL;
//so i's first intron starts AFTER j's first intron
// then j must contain i, so i's last intron must end with or before j's last intron
if (ti.exons[imax]->start>tj.exons[jmax]->start) return NULL;
//comment out the line above if you just want "intron compatibility" (i.e. extension of intron chains )
}
else if (i>j) {
//j==1, tj's start must not conflict with the previous intron of ti
if (tj.start<ti.exons[i-1]->start) return NULL;
//so j's intron chain starts AFTER i's
// then i must contain j, so j's last intron must end with or before j's last intron
if (tj.exons[jmax]->start>ti.exons[imax]->start) return NULL;
//comment out the line above for just "intronCompatible()" check (allowing extension of intron chain)
}
//now check if the rest of the introns overlap, in the same sequence
i++;
j++;
while (i<=imax && j<=jmax) {
if (ti.exons[i-1]->end!=tj.exons[j-1]->end ||
ti.exons[i]->start!=tj.exons[j]->start) return NULL;
i++;
j++;
}
i--;
j--;
if (i==imax && j<jmax) {
// tj has more introns to the right, check if ti's end doesn't conflict with the current tj exon boundary
if (ti.end>tj.exons[j]->end) return NULL;
}
else if (j==jmax && i<imax) {
if (tj.end>ti.exons[i]->end) return NULL;
}
return bigger;
}
int gseqCmpName(const pointer p1, const pointer p2) {
return strcmp(((GenomicSeqData*)p1)->gseq_name, ((GenomicSeqData*)p2)->gseq_name);
}
void printLocus(GffLocus* loc, const char* pre) {
if (pre!=NULL) fprintf(stderr, "%s", pre);
GMessage(" [%d-%d] : ", loc->start, loc->end);
GMessage("%s",loc->rnas[0]->getID());
for (int i=1;i<loc->rnas.Count();i++) {
GMessage(",%s",loc->rnas[i]->getID());
}
GMessage("\n");
}
void preserveContainedCDS(GffObj* t, GffObj* tfrom) {
//transfer CDS info to the container t if it's a larger protein
if (tfrom->CDstart==0) return;
if (t->CDstart) {
if (tfrom->CDstart<t->CDstart && tfrom->CDstart>=t->start)
t->CDstart=tfrom->CDstart;
if (tfrom->CDend>t->CDend && tfrom->CDend<=t->end)
t->CDend=tfrom->CDend;
}
else { //no CDS info on container, just copy it from the contained
t->addCDS(tfrom->CDstart, tfrom->CDend, tfrom->CDphase);
}
}
bool exonOverlap2Gene(GffObj* t, GffObj& g) {
if (t->exons.Count()>0) {
return t->exonOverlap(g.start, g.end);
}
else return g.overlap(*t);
}
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;
}
void collectLocusData(GList<GenomicSeqData>& ref_data) {
int locus_num=0;
for (int g=0;g<ref_data.Count();g++) {
GenomicSeqData* gdata=ref_data[g];
for (int l=0;l<gdata->loci.Count();l++) {
GffLocus& loc=*(gdata->loci[l]);
GHash<int> gnames(true); //gene names in this locus
GHash<int> geneids(true); //Entrez GeneID: numbers
for (int i=0;i<loc.rnas.Count();i++) {
GffObj& t=*(loc.rnas[i]);
GStr gname(t.getGeneName());
if (!gname.is_empty()) {
gname.upper();
int* prevg=gnames.Find(gname.chars());
if (prevg!=NULL) (*prevg)++;
else gnames.Add(gname, new int(1));
}
//parse GeneID xrefs, if any:
GStr xrefs(t.getAttr("xrefs"));
if (!xrefs.is_empty()) {
xrefs.startTokenize(",");
GStr token;
while (xrefs.nextToken(token)) {
token.upper();
if (token.startsWith("GENEID:")) {
token.cut(0,token.index(':')+1);
int* prevg=geneids.Find(token.chars());
if (prevg!=NULL) (*prevg)++;
else geneids.Add(token, new int(1));
}
} //for each xref
} //xrefs parsing
}//for each transcript
locus_num++;
loc.locus_num=locus_num;
if (gnames.Count()>0) { //collect all gene names associated to this locus
gnames.startIterate();
int* gfreq=NULL;
char* key=NULL;
while ((gfreq=gnames.NextData(key))!=NULL) {
loc.gene_names.AddIfNew(new CGeneSym(key,*gfreq));
}
} //added collected gene_names
if (loc.gene_ids.Count()>0) { //collect all GeneIDs names associated to this locus
geneids.startIterate();
int* gfreq=NULL;
char* key=NULL;
while ((gfreq=geneids.NextData(key))!=NULL) {
loc.gene_ids.AddIfNew(new CGeneSym(key,*gfreq));
}
}
} //for each locus
}//for each genomic sequence
}
void GffLoader::load(GList<GenomicSeqData>& seqdata, GFValidateFunc* gf_validate,
bool doCluster, bool doCollapseRedundant,
bool matchAllIntrons, bool fuzzSpan, bool forceExons) {
GffReader* gffr=new GffReader(f, this->transcriptsOnly, false); //not only mRNA features, not sorted
gffr->showWarnings(this->showWarnings);
// keepAttrs mergeCloseExons noExonAttr
gffr->readAll(this->fullAttributes, this->mergeCloseExons, this->noExonAttrs);
GVec<int> pseudoAttrIds;
GVec<int> pseudoFeatureIds;
if (this->noPseudo) {
GffNameList& fnames = gffr->names->feats;
for (int i=0;i<fnames.Count();i++) {
char* n=fnames[i]->name;
if (startsWith(n, "pseudo")) {
pseudoFeatureIds.Add(fnames[i]->idx);
}
}
GffNameList& attrnames = gffr->names->attrs;
for (int i=0;i<attrnames.Count();i++) {
char* n=attrnames[i]->name;
char* p=strifind(n, "pseudo");
if (p==n || (p==n+2 && tolower(n[0])=='i' && tolower(n[1])=='s')) {
pseudoAttrIds.Add(attrnames[i]->idx);
}
}
}
//int redundant=0; //redundant annotation discarded
if (verbose) GMessage(" .. loaded %d genomic features from %s\n", gffr->gflst.Count(), fname.chars());
//int rna_deleted=0;
//add to GenomicSeqData, adding to existing loci and identifying intron-chain duplicates
for (int k=0;k<gffr->gflst.Count();k++) {
GffObj* m=gffr->gflst[k];
if (strcmp(m->getFeatureName(), "locus")==0 &&
m->getAttr("transcripts")!=NULL) {
continue; //discard locus meta-features
}
if (this->noPseudo) {
bool is_pseudo=false;
for (int i=0;i<pseudoFeatureIds.Count();++i) {
if (pseudoFeatureIds[i]==m->ftype_id) {
is_pseudo=true;
break;
}
}
if (is_pseudo) continue;
for (int i=0;i<pseudoAttrIds.Count();++i) {
char* attrv=NULL;
if (m->attrs!=NULL) attrv=m->attrs->getAttr(pseudoAttrIds[i]);
if (attrv!=NULL) {
char fc=tolower(attrv[0]);
if (fc=='t' || fc=='y' || fc=='1') {
is_pseudo=true;
break;
}
}
}
if (is_pseudo) continue;
//last resort:
// scan all the attribute values for "pseudogene" keyword (NCBI does that for "product" attr)
/*
if (m->attrs!=NULL) {
for (int i=0;i<m->attrs->Count();++i) {
GffAttr& a=*(m->attrs->Get(i));
if (strifind(a.attr_val, "pseudogene")) {
is_pseudo=true;
break;
}
}
}
if (is_pseudo) continue;
*/
} //pseudogene detection requested
char* rloc=m->getAttr("locus");
if (rloc!=NULL && startsWith(rloc, "RLOC_")) {
m->removeAttr("locus", rloc);
}
/*
if (m->exons.Count()==0 && m->children.Count()==0) {
//a non-mRNA feature with no subfeatures
//add a dummy exon just to have the generic exon checking work
m->addExon(m->start,m->end);
}
*/
if (forceExons) { // && m->children.Count()==0) {
m->exon_ftype_id=gff_fid_exon;
}
//GList<GffObj> gfadd(false,false); -- for gf_validate()?
if (gf_validate!=NULL && !(*gf_validate)(m, NULL)) {
continue;
}
m->isUsed(true); //so the gffreader won't destroy it
int i=-1;
GenomicSeqData f(m->gseq_id);
GenomicSeqData* gdata=NULL;
if (seqdata.Found(&f,i)) gdata=seqdata[i];
else { //entry not created yet for this genomic seq
gdata=new GenomicSeqData(m->gseq_id);
seqdata.Add(gdata);
}
/*
for (int k=0;k<gfadd.Count();k++) {
bool keep=placeGf(gfadd[k], gdata, doCluster, doCollapseRedundant, matchAllIntrons, fuzzSpan);
if (!keep) {
gfadd[k]->isUsed(false);
//DEBUG
GMessage("Feature %s(%d-%d) is going to be discarded..\n",gfadd[k]->getID(), gfadd[k]->start, gfadd[k]->end);
}
}
*/
bool keep=placeGf(m, gdata, doCluster, doCollapseRedundant, matchAllIntrons, fuzzSpan);
if (!keep) {
m->isUsed(false);
//DEBUG
//GMessage("Feature %s(%d-%d) is going to be discarded..\n",m->getID(), m->start, m->end);
}
} //for each read gffObj
//if (verbose) GMessage(" .. %d records from %s clustered into loci.\n", gffr->gflst.Count(), fname.chars());
if (f!=stdin) { fclose(f); f=NULL; }
delete gffr;
}