// Add records the SAM record as having being located at the given chunk.
func (i *Index) Add(r Record, c bgzf.Chunk, placed, mapped bool) error {
refName := r.RefName()
rid, ok := i.nameMap[refName]
if !ok {
rid = len(i.refNames)
i.refNames = append(i.refNames, refName)
}
shim := tabixShim{id: rid, start: r.Start(), end: r.End()}
return i.idx.Add(shim, internal.BinFor(r.Start(), r.End()), c, placed, mapped)
}
// Bin returns the BAM index bin of the record.
func (r *Record) Bin() int {
if r.Flags&Unmapped != 0 {
return 4680 // reg2bin(-1, 0)
}
end := r.End()
if !internal.IsValidIndexPos(r.Pos) || !internal.IsValidIndexPos(end) {
return -1
}
return int(internal.BinFor(r.Pos, r.End()))
}
