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misspellings penality -> pelnalty

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This commit is contained in:
Eric Coissac
2025-01-09 07:22:23 +01:00
parent c58d9772ac
commit becb995e3d
3 changed files with 19 additions and 19 deletions
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18
pkg/obitools/obikmersim/options.go
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@ -15,8 +15,8 @@ var _MinSharedKmers = 1
var _Self = false
var _Delta = 5
var _PenalityScale = 1.0
var _GapPenality = 2.0
var _PenaltyScale = 1.0
var _GapPenalty = 2.0
var _FastScoreAbs = false
var _KmerMaxOccur = -1
@ -62,13 +62,13 @@ func KmerSimMatchOptionSet(options *getoptions.GetOpt) {
options.Alias("d"),
options.Description("Delta value for the match."))
options.Float64Var(&_PenalityScale, "penality-scale", _PenalityScale,
options.Float64Var(&_PenaltyScale, "penalty-scale", _PenaltyScale,
options.Alias("X"),
options.Description("Scale factor applied to the mismatch score and the gap penality (default 1)."))
options.Description("Scale factor applied to the mismatch score and the gap penalty (default 1)."))
options.Float64Var(&_GapPenality, "gap-penality", _GapPenality,
options.Float64Var(&_GapPenalty, "gap-penalty", _GapPenalty,
options.Alias("G"),
options.Description("Gap penality expressed as the multiply factor applied to the mismatch score between two nucleotides with a quality of 40 (default 2)."))
options.Description("Gap penalty expressed as the multiply factor applied to the mismatch score between two nucleotides with a quality of 40 (default 2)."))
options.BoolVar(&_FastScoreAbs, "fast-absolute", _FastScoreAbs,
options.Alias("a"),
@ -129,15 +129,15 @@ func CLIDelta() int {
}
func CLIScale() float64 {
return _PenalityScale
return _PenaltyScale
}
func CLIGapPenality() float64 {
return _GapPenality
return _GapPenalty
}
func CLIGap() float64 {
return _GapPenality
return _GapPenalty
}
func CLIFastRelativeScore() bool {

16
pkg/obitools/obipairing/options.go
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@ -10,12 +10,12 @@ var _ForwardFile = ""
var _ReverseFile = ""
var _Delta = 5
var _MinOverlap = 20
var _GapPenality = 2.0
var _GapPenalty = 2.0
var _WithoutStats = false
var _MinIdentity = 0.9
var _NoFastAlign = false
var _FastScoreAbs = false
var _PenalityScale = 1.0
var _PenaltyScale = 1.0
func PairingOptionSet(options *getoptions.GetOpt) {
options.StringVar(&_ForwardFile, "forward-reads", "",
@ -36,11 +36,11 @@ func PairingOptionSet(options *getoptions.GetOpt) {
options.Float64Var(&_MinIdentity, "min-identity", _MinIdentity,
options.Alias("X"),
options.Description("Minimum identity between ovelaped regions of the reads to consider the aligment"))
options.Float64Var(&_GapPenality, "gap-penality", _GapPenality,
options.Float64Var(&_GapPenalty, "gap-penalty", _GapPenalty,
options.Alias("G"),
options.Description("Gap penality expressed as the multiply factor applied to the mismatch score between two nucleotides with a quality of 40 (default 2)."))
options.Float64Var(&_PenalityScale, "penality-scale", _PenalityScale,
options.Description("Scale factor applied to the mismatch score and the gap penality (default 1)."))
options.Description("Gap penaity expressed as the multiply factor applied to the mismatch score between two nucleotides with a quality of 40 (default 2)."))
options.Float64Var(&_PenaltyScale, "penalty-scale", _PenaltyScale,
options.Description("Scale factor applied to the mismatch score and the gap penalty (default 1)."))
options.BoolVar(&_WithoutStats, "without-stat", _WithoutStats,
options.Alias("S"),
options.Description("Remove alignment statistics from the produced consensus sequences."))
@ -85,11 +85,11 @@ func CLIMinIdentity() float64 {
}
func CLIGapPenality() float64 {
return _GapPenality
return _GapPenalty
}
func CLIPenalityScale() float64 {
return _PenalityScale
return _PenaltyScale
}
func CLIWithStats() bool {

4
pkg/obitools/obipairing/pairing.go
View File

@ -85,7 +85,7 @@ func JoinPairedSequence(seqA, seqB *obiseq.BioSequence, inplace bool) *obiseq.Bi
//
// - seqA, seqB: the pair of sequences to align.
//
// - gap: the gap penality is expressed as a multiplicator factor of the cost
// - gap: the gap penalty is expressed as a multiplicator factor of the cost
// of a mismatch between two bases having a quality score of 40.
//
// - delta: the extension in number of base pairs added on both sides of the
@ -192,7 +192,7 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
// - iterator: is an iterator of paired sequences as produced by the method
// IBioSequenceBatch.PairWith
//
// - gap: the gap penality is expressed as a multiplicator factor of the cost
// - gap: the gap penalty is expressed as a multiplicator factor of the cost
// of a mismatch between two bases having a quality score of 40.
//
// - delta: the extension in number of base pairs added on both sides of the