From 3b5d4ba4555cfad09fad4cfcbda48ca0f23b750d Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Tue, 11 Mar 2025 16:35:38 +0100
Subject: [PATCH] patch a bug in obiannotate

---
 pkg/obiiter/workers.go    |  5 +++++
 pkg/obioptions/version.go |  2 +-
 pkg/obiseq/worker.go      | 35 +++++++++++++++++++++++++++++++++++
 3 files changed, 41 insertions(+), 1 deletion(-)

diff --git a/pkg/obiiter/workers.go b/pkg/obiiter/workers.go
index 6320737..ca9465c 100644
--- a/pkg/obiiter/workers.go
+++ b/pkg/obiiter/workers.go
@@ -63,6 +63,11 @@ func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePre
 //
 // The function returns a new IBioSequence containing the modified slices.
 func (iterator IBioSequence) MakeISliceWorker(worker obiseq.SeqSliceWorker, breakOnError bool, sizes ...int) IBioSequence {
+
+	if worker == nil {
+		return iterator
+	}
+
 	nworkers := obidefault.ParallelWorkers()
 
 	if len(sizes) > 0 {
diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go
index 4fab2a9..6d67e4b 100644
--- a/pkg/obioptions/version.go
+++ b/pkg/obioptions/version.go
@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "52d5f6f"
+var _Commit = "50d11ce"
 var _Version = "Release 4.4.0"
 
 // Version returns the version of the obitools package.
diff --git a/pkg/obiseq/worker.go b/pkg/obiseq/worker.go
index fcafd22..4c0c04a 100644
--- a/pkg/obiseq/worker.go
+++ b/pkg/obiseq/worker.go
@@ -133,6 +133,34 @@ func SeqToSliceWorker(worker SeqWorker,
 	return f
 }
 
+func SeqToSliceFilterOnWorker(condition SequencePredicate,
+	breakOnError bool) SeqSliceWorker {
+
+	if condition == nil {
+		return func(slice BioSequenceSlice) (BioSequenceSlice, error) {
+			return slice, nil
+		}
+	}
+
+	f := func(input BioSequenceSlice) (BioSequenceSlice, error) {
+		output := MakeBioSequenceSlice(len(input))
+
+		i := 0
+
+		for _, s := range input {
+			if condition(s) {
+				output[i] = s
+				i++
+			}
+		}
+
+		return output[0:i], nil
+	}
+
+	return f
+
+}
+
 // SeqToSliceConditionalWorker creates a new SeqSliceWorker that processes each sequence in a slice based on a condition. It takes a SequencePredicate and a worker function as arguments. The worker function is only applied to sequences that satisfy the condition.
 // If `condition` is nil, this function just behaves like SeqToSliceWorker with the provided `worker`.
 // If `breakOnError` is true, the pipeline will stop and return an error if any sequence processing fails. Otherwise, it will log a warning message for each failed sequence.
@@ -153,6 +181,10 @@ func SeqToSliceConditionalWorker(
 		return SeqToSliceWorker(worker, breakOnError)
 	}
 
+	if worker == nil {
+		return nil
+	}
+
 	f := func(input BioSequenceSlice) (BioSequenceSlice, error) {
 		output := MakeBioSequenceSlice(len(input))
 
@@ -180,6 +212,9 @@ func SeqToSliceConditionalWorker(
 							s.Id(), err)
 					}
 				}
+			} else {
+				output[i] = s
+				i++
 			}
 		}