func (t *Tbx) getChrom(chrom string) C.int {
t.mu.RLock()
if i, ok := t.chromCache[chrom]; ok {
t.mu.RUnlock()
return i
}
t.mu.RUnlock()
cchrom := C.CString(chrom)
ichrom := C.tbx_name2id(t.tbx, cchrom)
C.free(unsafe.Pointer(cchrom))
if ichrom == -1 {
if strings.HasPrefix(chrom, "chr") {
cchrom = C.CString(chrom[3:])
} else {
cchrom = C.CString("chr" + chrom)
}
ichrom = C.tbx_name2id(t.tbx, cchrom)
C.free(unsafe.Pointer(cchrom))
}
t.mu.Lock()
t.chromCache[chrom] = ichrom
t.mu.Unlock()
return ichrom
}
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
}