RleIter(RObject& rle):
rlens(as<IntegerVector>(rle.slot("lengths"))),
values(as<IntegerVector>(rle.slot("values"))),
names(as<CharacterVector>(values.attr("levels"))),
run(0), rpos(-1)
{
next();
}
//parses the GR object.
void parseRegions(std::vector<GArray>& container, RObject& gr, samfile_t* in){
if (not gr.inherits("GRanges"))
stop("must provide a GRanges object");
IntegerVector starts = as<IntegerVector>(as<RObject>(gr.slot("ranges")).slot("start"));
IntegerVector lens = as<IntegerVector>(as<RObject>(gr.slot("ranges")).slot("width"));
RObject chrsRle = as<RObject>(gr.slot("seqnames"));
RObject strandsRle = as<RObject>(gr.slot("strand"));
RleIter chrs(chrsRle);
RleIter strands(strandsRle);
container.reserve(container.size() + starts.length());
Iint e_starts = starts.end(); Iint i_starts = starts.begin(); Iint i_lens = lens.begin();
int lastStrandRun = -1;
int strand = -1;
int lastChrsRun = -1;
int rid = -1;
for (; i_starts < e_starts; ++i_starts, ++i_lens, chrs.next(), strands.next()){
//if new run, update chromosome
if (lastChrsRun != chrs.run){
lastChrsRun = chrs.run;
rid = getRefId(in, chrs.getValue());
if (rid == -1)
stop("chromosome " + (std::string)chrs.getValue() + " not present in the bam file");
}
//if new run, update strand
if (lastStrandRun != strands.run){
lastStrandRun = strands.run;
const std::string& s = strands.getValue();
if (s == "-"){ strand = -1; }
else if (s == "+"){ strand = +1; }
else { strand = 0; }
}
container.push_back(GArray(rid, *i_starts - 1, *i_lens, strand));
}
}
