Exemple #1
0
func New(path string, n ...int) (*Tbx, error) {
	if !(xopen.Exists(path) && (xopen.Exists(path+".tbi") || xopen.Exists(path+".csi"))) {
		return nil, fmt.Errorf("need gz file and .tbi for %s", path)
	}
	size := 20
	if len(n) > 0 {
		size = n[0]
	}

	t := &Tbx{path: path}
	cs, mode := C.CString(t.path), C.char('r')
	defer C.free(unsafe.Pointer(cs))

	t.htfs = make(chan *C.htsFile, size)
	for i := 0; i < cap(t.htfs); i++ {
		t.htfs <- C.hts_open(cs, &mode)
	}

	t.kCache = make(chan C.kstring_t, size*2)
	for i := 0; i < cap(t.kCache); i++ {
		t.kCache <- C.kstring_t{}
	}
	t.chromCache = make(map[string]C.int)

	if xopen.Exists(path + ".csi") {
		csi := C.CString(path + ".csi")
		defer C.free(unsafe.Pointer(csi))
		t.tbx = C.tbx_index_load2(cs, csi)
	} else {
		t.tbx = C.tbx_index_load(cs)
	}
	runtime.SetFinalizer(t, _close)

	return t, nil
}
Exemple #2
0
// New takes a path to a bgziped (and tabixed file) and returns the tabix struct.
func New(path string) (*Tabix, error) {
	if !(xopen.Exists(path) && xopen.Exists(path+".tbi")) {
		return nil, fmt.Errorf("need gz file and .tbi for %s", path)
	}

	t := &Tabix{path: path}
	cs := C.CString(t.path)
	defer C.free(unsafe.Pointer(cs))
	mode := C.char('r')
	t.htf = C.hts_open(cs, &mode)
	t.tbx = C.tbx_index_load(cs)
	runtime.SetFinalizer(t, tabixCloser)
	if strings.HasSuffix(path, ".bed.gz") {
		t.typ = BED
	} else if strings.HasSuffix(path, ".vcf.gz") {
		t.hdr = C.bcf_hdr_read(t.htf)
		t.typ = VCF
	} else {
		t.typ = OTHER
	}
	t.original_header = true
	return t, nil
}