From e775f7e256e22426a329fb33a817d486ed340f36 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Tue, 10 Feb 2026 09:36:32 +0100
Subject: [PATCH] Add option to keep shorter fragments in lowmask

Add a new boolean option 'keep-shorter' to preserve fragments shorter than kmer-size during split/extract mode.

This change introduces a new flag _lowmaskKeepShorter that controls whether fragments
shorter than the kmer size should be kept during split/extract operations.

The implementation:
1. Adds the new boolean variable _lowmaskKeepShorter
2. Registers the command-line option "keep-shorter"
3. Updates the lowMaskWorker function signature to accept the keepShorter parameter
4. Modifies the fragment selection logic to check the keepShorter flag
5. Updates the worker creation to pass the global flag value

This allows users to control the behavior when dealing with short sequences in
split/extract modes, providing more flexibility in low-complexity masking.
---
 pkg/obitools/obik/lowmask.go | 62 +++++++++++++++++++++++++-----------
 1 file changed, 43 insertions(+), 19 deletions(-)

diff --git a/pkg/obitools/obik/lowmask.go b/pkg/obitools/obik/lowmask.go
index 014a160..7710c1e 100644
--- a/pkg/obitools/obik/lowmask.go
+++ b/pkg/obitools/obik/lowmask.go
@@ -32,6 +32,7 @@ var _lowmaskThreshold = 0.5
 var _lowmaskSplitMode = false
 var _lowmaskLowMode = false
 var _lowmaskMaskChar = "."
+var _lowmaskKeepShorter = false
 
 // LowMaskOptionSet registers options specific to low-complexity masking.
 func LowMaskOptionSet(options *getoptions.GetOpt) {
@@ -52,6 +53,9 @@ func LowMaskOptionSet(options *getoptions.GetOpt) {
 
 	options.StringVar(&_lowmaskMaskChar, "masking-char", _lowmaskMaskChar,
 		options.Description("Character used to mask low complexity regions."))
+
+	options.BoolVar(&_lowmaskKeepShorter, "keep-shorter", _lowmaskKeepShorter,
+		options.Description("Keep fragments shorter than kmer-size in split/extract mode."))
 }
 
 func lowmaskMaskingMode() MaskingMode {
@@ -74,7 +78,7 @@ func lowmaskMaskingChar() byte {
 }
 
 // lowMaskWorker creates a worker to mask low-complexity regions in DNA sequences.
-func lowMaskWorker(kmer_size int, level_max int, threshold float64, mode MaskingMode, maskChar byte) obiseq.SeqWorker {
+func lowMaskWorker(kmer_size int, level_max int, threshold float64, mode MaskingMode, maskChar byte, keepShorter bool) obiseq.SeqWorker {
 
 	nLogN := make([]float64, kmer_size+1)
 	for i := 1; i <= kmer_size; i++ {
@@ -301,11 +305,14 @@ func lowMaskWorker(kmer_size int, level_max int, threshold float64, mode Masking
 			}
 			if inlow && !masked {
 				if fromlow >= 0 {
-					frg, err := sequence.Subsequence(fromlow, i, false)
-					if err != nil {
-						return nil, err
+					frgLen := i - fromlow
+					if keepShorter || frgLen >= kmer_size {
+						frg, err := sequence.Subsequence(fromlow, i, false)
+						if err != nil {
+							return nil, err
+						}
+						rep.Push(frg)
 					}
-					rep.Push(frg)
 				}
 				inlow = false
 				fromlow = -1
@@ -313,11 +320,14 @@ func lowMaskWorker(kmer_size int, level_max int, threshold float64, mode Masking
 		}
 
 		if inlow && fromlow >= 0 {
-			frg, err := sequence.Subsequence(fromlow, len(maskPosition), false)
-			if err != nil {
-				return nil, err
+			frgLen := len(maskPosition) - fromlow
+			if keepShorter || frgLen >= kmer_size {
+				frg, err := sequence.Subsequence(fromlow, len(maskPosition), false)
+				if err != nil {
+					return nil, err
+				}
+				rep.Push(frg)
 			}
-			rep.Push(frg)
 		}
 
 		return *rep, nil
@@ -335,11 +345,14 @@ func lowMaskWorker(kmer_size int, level_max int, threshold float64, mode Masking
 			}
 			if inhigh && masked {
 				if fromhigh >= 0 {
-					frg, err := sequence.Subsequence(fromhigh, i, false)
-					if err != nil {
-						return nil, err
+					frgLen := i - fromhigh
+					if keepShorter || frgLen >= kmer_size {
+						frg, err := sequence.Subsequence(fromhigh, i, false)
+						if err != nil {
+							return nil, err
+						}
+						rep.Push(frg)
 					}
-					rep.Push(frg)
 				}
 				inhigh = false
 				fromhigh = -1
@@ -347,11 +360,14 @@ func lowMaskWorker(kmer_size int, level_max int, threshold float64, mode Masking
 		}
 
 		if inhigh && fromhigh >= 0 {
-			frg, err := sequence.Subsequence(fromhigh, len(maskPosition), false)
-			if err != nil {
-				return nil, err
+			frgLen := len(maskPosition) - fromhigh
+			if keepShorter || frgLen >= kmer_size {
+				frg, err := sequence.Subsequence(fromhigh, len(maskPosition), false)
+				if err != nil {
+					return nil, err
+				}
+				rep.Push(frg)
 			}
-			rep.Push(frg)
 		}
 
 		return *rep, nil
@@ -364,7 +380,15 @@ func lowMaskWorker(kmer_size int, level_max int, threshold float64, mode Masking
 			for i := range remove {
 				remove[i] = true
 			}
-			return applyMaskMode(sequence, remove, maskChar)
+			switch mode {
+			case MaskMode:
+				return applyMaskMode(sequence, remove, maskChar)
+			case SplitMode:
+				return selectunmasked(sequence, remove)
+			case ExtractMode:
+				return selectMasked(sequence, remove)
+			}
+			return nil, fmt.Errorf("unknown mode %d", mode)
 		}
 
 		bseq := sequence.Sequence()
@@ -442,7 +466,7 @@ func runLowmask(ctx context.Context, opt *getoptions.GetOpt, args []string) erro
 		return fmt.Errorf("failed to open sequence files: %w", err)
 	}
 
-	worker := lowMaskWorker(kmerSize, levelMax, threshold, mode, maskChar)
+	worker := lowMaskWorker(kmerSize, levelMax, threshold, mode, maskChar, _lowmaskKeepShorter)
 
 	masked := sequences.MakeIWorker(
 		worker,