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package vcfgo
func leftalign(pos int, ref []byte, alt []byte, seq []byte) (int, []byte, []byte, error) {
/* actually this isn't necessary
if !bytes.HasSuffix(seq, ref) {
return 0, ref, alt, errors.New("leftalign: sequence should end with ref")
}
*/
subseq := seq[:len(seq)-len(ref)]
quit := false
j := len(subseq)
for j > 0 && !quit {
quit = true
if ref[len(ref)-1] == alt[len(alt)-1] {
ref = ref[:len(ref)-1]
alt = alt[:len(alt)-1]
quit = false
}
if len(ref) == 0 || len(alt) == 0 {
j--
// use j + 1 to get a slice.
ref = append(subseq[j:j+1], ref...)
alt = append(subseq[j:j+1], alt...)
quit = false
}
}
return pos - (len(subseq) - j), ref, alt, nil
}
func lefttrim(pos int, ref []byte, alt []byte) (int, []byte, []byte, error) {
if 1 == len(ref) && len(alt) == 1 {
return pos, ref, alt, nil
}
n := 0
minLen := len(ref)
if len(alt) < minLen {
minLen = len(alt)
}
for n+1 < minLen && alt[n] == ref[n] {
n++
}
alt, ref = alt[n:], ref[n:]
pos += n
return pos, ref, alt, nil
}
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