std::string GenomicRegion::ChrName(const BamHeader& h) const {
std::string cc;
if (!h.isEmpty()) {
if (chr >= h.NumSequences())
throw std::invalid_argument( "GenomicRegion::ChrName - not enough targets in BamHeader to cover ref id");
else
cc = h.IDtoName(chr); // std::string(h->target_name[chr]);
} else {
cc = chrToString(chr);
}
return cc;
}
GenomicRegion::GenomicRegion(const std::string& reg, const BamHeader& hdr) {
if (hdr.isEmpty())
throw std::invalid_argument("GenomicRegion constructor - supplied empty BamHeader");
// scrub String
//std::string reg2 = SeqLib::scrubString(reg, "chr");
// use htslib region parsing code
int tid, beg, end;
const char * q = hts_parse_reg(reg.c_str(), &beg, &end);
if (q) {
char *tmp = (char*)alloca(q - reg.c_str() + 1); // stack alloc
strncpy(tmp, reg.c_str(), q - reg.c_str());
tmp[q - reg.c_str()] = 0;
tid = hdr.Name2ID(std::string(tmp)); //bam_name2id(h.get(), tmp);
if (tid < 0) {
std::string inv = "GenomicRegion constructor: Failed to set region for " + reg;
throw std::invalid_argument(inv);
}
if (end == INT_MAX) { // single chrome
tid = hdr.Name2ID(reg);
beg = 0;
end = hdr.GetSequenceLength(reg);
}
} else {
std::string inv = "GenomicRegion constructor: Failed to set region for " + reg;
throw std::invalid_argument(inv);
}
chr = tid;
pos1 = beg+1;
pos2 = end;
strand = '*';
}
