// ReadIndex reads the BAI Index from the given io.Reader.
func ReadIndex(r io.Reader) (*Index, error) {
var (
idx Index
magic [4]byte
err error
)
err = binary.Read(r, binary.LittleEndian, &magic)
if err != nil {
return nil, err
}
if magic != baiMagic {
return nil, errors.New("bam: magic number mismatch")
}
var n int32
err = binary.Read(r, binary.LittleEndian, &n)
if err != nil {
return nil, err
}
if n == 0 {
return nil, nil
}
idx.idx, err = internal.ReadIndex(r, n, "bam")
if err != nil {
return nil, err
}
return &idx, nil
}
// ReadFrom reads the tabix index from the given io.Reader. Note that
// the tabix specification states that the index is stored as BGZF, but
// ReadFrom does not perform decompression.
func ReadFrom(r io.Reader) (*Index, error) {
var (
idx Index
magic [4]byte
err error
)
err = binary.Read(r, binary.LittleEndian, &magic)
if err != nil {
return nil, err
}
if magic != tbiMagic {
return nil, errors.New("tabix: magic number mismatch")
}
var n int32
err = binary.Read(r, binary.LittleEndian, &n)
if err != nil {
return nil, err
}
if n == 0 {
return nil, nil
}
err = readTabixHeader(r, &idx)
if err != nil {
return nil, err
}
if len(idx.refNames) != int(n) {
return nil, fmt.Errorf("tabix: name count mismatch: %d != %d", len(idx.refNames), n)
}
idx.nameMap = make(map[string]int)
for i, n := range idx.refNames {
idx.nameMap[n] = i
}
idx.idx, err = internal.ReadIndex(r, n, "tabix")
if err != nil {
return nil, err
}
return &idx, nil
}
