func (tbx *Bix) Query(region interfaces.IPosition) (interfaces.RelatableIterator, error) {
tbx2, err := newShort(tbx)
if err != nil {
return nil, err
}
if region == nil {
var l string
var err error
buf := bufio.NewReader(tbx2.bgzf)
l, err = buf.ReadString('\n')
for i := 0; i < int(tbx2.Index.Skip) || rune(l[0]) == tbx2.Index.MetaChar; i++ {
l, err = buf.ReadString('\n')
if err != nil {
return nil, err
}
}
if tbx2.Index.Skip == 0 && rune(l[0]) != tbx2.Index.MetaChar {
buf = bufio.NewReader(io.MultiReader(strings.NewReader(l), buf))
}
return bixerator{nil, buf, tbx2, region}, nil
}
cr, err := tbx2.ChunkedReader(region.Chrom(), int(region.Start()), int(region.End()))
if err != nil {
if cr != nil {
tbx2.Close()
cr.Close()
}
return nil, err
}
return bixerator{cr, bufio.NewReader(cr), tbx2, region}, nil
}
func (t *Tabix) Get(q interfaces.IPosition) []interfaces.IPosition {
//cs := C.CString(fmt.Sprintf("%s:%d-%d", q.Chrom(), q.Start()+1, q.End()))
ch := C.CString(q.Chrom())
cs := C.tbx_name2id(t.tbx, ch)
itr := C.tabix_itr_queryi(t.tbx, cs, C.int(q.Start()), C.int(q.End()))
kstr := C.kstring_t{}
overlaps := make([]interfaces.IPosition, 0, 4)
l := C.int(10)
for l > 0 {
l := C.atbx_itr_next(t.htf, t.tbx, itr, &kstr)
if l < 0 {
break
}
//res := C.GoString(kstr.s)
if t.typ == VCF {
b := C.bcf_init()
ret := C.vcf_parse(&kstr, t.hdr, b)
if ret < 0 {
log.Printf("error parsing %s\n", C.GoStringN(kstr.s, C.int(kstr.l)))
}
overlaps = append(overlaps, NewVariant(b, t.hdr, 1))
} else if t.typ == BED {
iv, err := parsers.IntervalFromBedLine(C.GoBytes(unsafe.Pointer(kstr.s), C.int(kstr.l)))
if err != nil {
log.Printf("error parsing %s:%s\n", C.GoStringN(kstr.s, C.int(kstr.l)), err)
}
if iv != nil {
overlaps = append(overlaps, iv)
}
}
}
C.hts_itr_destroy(itr)
C.free(unsafe.Pointer(ch))
C.free(unsafe.Pointer(kstr.s))
return overlaps
}
// don't need to use chrom since we are only testing things
// returned from irelate.IRelate.
func overlap(a, b interfaces.IPosition) bool {
return b.Start() < a.End() && a.Start() < b.End()
}
