func (t *Tbx) Get(chrom string, start int, end int) (io.Reader, error) {
ichrom := t.getChrom(chrom)
if ichrom == -1.0 {
log.Printf("chromosome: %s not found in %s \n", chrom, t.path)
return strings.NewReader(""), nil
}
ret := C.int(1)
itr := C.tabix_itr_queryi(t.tbx, ichrom, C.int(start), C.int(end), &ret)
if ret < 0 {
return strings.NewReader(""), nil
}
p := newPipe(1)
go func() {
l := C.int(10)
kstr1, kstr2 := <-t.kCache, <-t.kCache
htf := <-t.htfs
for l > 0 {
// < 0 means no data
// == 0 means we got data, but end after this
l = C.tbx_itr_next5(htf, t.tbx, itr, &kstr1, &kstr2)
if l < 0 {
break
}
res := C.GoBytes(unsafe.Pointer(kstr1.s), C.int(kstr1.l))
_, err := p.Write(res)
if err != nil {
log.Fatal(err)
}
}
close(p.ch)
// unlock
t.htfs <- htf
t.kCache <- kstr1
t.kCache <- kstr2
}()
return p, 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
}