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Changes to be committed:

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modified:   Release-notes.md
	modified:   pkg/obialign/pairedendalign.go
	modified:   pkg/obilua/obiseq.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/biosequence.go
	modified:   pkg/obitools/obipairing/pairing.go
This commit is contained in:
Eric Coissac
2024-11-27 09:56:22 +01:00
parent 7884a74f9c
commit d29a56dcbf
6 changed files with 78 additions and 29 deletions
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54
pkg/obilua/obiseq.go
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@ -47,18 +47,21 @@ func newObiSeq(luaState *lua.LState) int {
}
var bioSequenceMethods = map[string]lua.LGFunction{
"id": bioSequenceGetSetId,
"sequence": bioSequenceGetSetSequence,
"qualities": bioSequenceGetSetQualities,
"definition": bioSequenceGetSetDefinition,
"count": bioSequenceGetSetCount,
"taxid": bioSequenceGetSetTaxid,
"attribute": bioSequenceGetSetAttribute,
"len": bioSequenceGetLength,
"has_sequence": bioSequenceHasSequence,
"has_qualities": bioSequenceHasQualities,
"source": bioSequenceGetSource,
"md5": bioSequenceGetMD5,
"id": bioSequenceGetSetId,
"sequence": bioSequenceGetSetSequence,
"qualities": bioSequenceGetSetQualities,
"definition": bioSequenceGetSetDefinition,
"count": bioSequenceGetSetCount,
"taxid": bioSequenceGetSetTaxid,
"attribute": bioSequenceGetSetAttribute,
"len": bioSequenceGetLength,
"has_sequence": bioSequenceHasSequence,
"has_qualities": bioSequenceHasQualities,
"source": bioSequenceGetSource,
"md5": bioSequenceGetMD5,
"md5_string": bioSequenceGetMD5String,
"subsequence": bioSequenceGetSubsequence,
"reverse_complement": bioSequenceGetRevcomp,
}
// checkBioSequence checks if the first argument in the Lua stack is a *obiseq.BioSequence.
@ -224,3 +227,30 @@ func bioSequenceGetMD5(luaState *lua.LState) int {
luaState.Push(rt)
return 1
}
func bioSequenceGetMD5String(luaState *lua.LState) int {
s := checkBioSequence(luaState)
md5 := s.MD5String()
luaState.Push(lua.LString(md5))
return 1
}
func bioSequenceGetSubsequence(luaState *lua.LState) int {
s := checkBioSequence(luaState)
start := luaState.CheckInt(2)
end := luaState.CheckInt(3)
subseq, err := s.Subsequence(start, end, false)
if err != nil {
luaState.RaiseError("%s : Error on subseq: %v", s.Id(), err)
return 0
}
luaState.Push(obiseq2Lua(luaState, subseq))
return 1
}
func bioSequenceGetRevcomp(luaState *lua.LState) int {
s := checkBioSequence(luaState)
revcomp := s.ReverseComplement(false)
luaState.Push(obiseq2Lua(luaState, revcomp))
return 1
}