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 tMatch(GffObj& a, GffObj& b, int& ovlen, bool fuzzunspl, bool contain_only) {
//strict intron chain match, or single-exon match
int imax=a.exons.Count()-1;
int jmax=b.exons.Count()-1;
ovlen=0;
if (imax!=jmax) return false; //different number of exons
if (imax==0) { //single-exon mRNAs
if (contain_only) {
return ((a.start>=b.start && a.end<=b.end) ||
(b.start>=a.start && b.end<=a.end));
}
if (fuzzunspl) {
//fuzz match for single-exon transfrags:
// it's a match if they overlap at least 80% of longest one
//ovlen=a.exons[0]->overlapLen(b.exons[0]);
//int maxlen=GMAX(a.covlen,b.covlen);
//return (ovlen>=maxlen*0.8);
return (singleExonTMatch(a,b,ovlen));
}
else {
//only exact match
ovlen=a.covlen;
return (a.exons[0]->start==b.exons[0]->start &&
a.exons[0]->end==b.exons[0]->end);
}
}
if ( a.exons[imax]->start<b.exons[0]->end ||
b.exons[jmax]->start<a.exons[0]->end )
return false; //intron chains do not overlap at all
//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
}
}
if (contain_only)
return ((a.start>=b.start && a.end<=b.end) ||
(b.start>=a.start && b.end<=a.end));
else return true;
}