From becb995e3d2fe66c14a33685172082138eae59b0 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Thu, 9 Jan 2025 07:22:23 +0100 Subject: [PATCH] misspellings penality -> pelnalty --- pkg/obitools/obikmersim/options.go | 18 +++++++++--------- pkg/obitools/obipairing/options.go | 16 ++++++++-------- pkg/obitools/obipairing/pairing.go | 4 ++-- 3 files changed, 19 insertions(+), 19 deletions(-) diff --git a/pkg/obitools/obikmersim/options.go b/pkg/obitools/obikmersim/options.go index de36922..eaef9da 100644 --- a/pkg/obitools/obikmersim/options.go +++ b/pkg/obitools/obikmersim/options.go @@ -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 { diff --git a/pkg/obitools/obipairing/options.go b/pkg/obitools/obipairing/options.go index a2b0666..0c524fd 100644 --- a/pkg/obitools/obipairing/options.go +++ b/pkg/obitools/obipairing/options.go @@ -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 { diff --git a/pkg/obitools/obipairing/pairing.go b/pkg/obitools/obipairing/pairing.go index 77613e4..a15e3ab 100644 --- a/pkg/obitools/obipairing/pairing.go +++ b/pkg/obitools/obipairing/pairing.go @@ -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