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
}
// 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
}