Example #1
0
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
}
Example #2
0
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
}