From 060f7db082c55150380f9042dd3711ef2a663764 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Thu, 2 Feb 2023 17:15:06 +0100
Subject: [PATCH] Adds code for the --length option of obiannotate

---
 pkg/obitools/obiannotate/obiannotate.go | 19 +++++++++++++++++--
 pkg/obitools/obiannotate/options.go     |  4 ++++
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/pkg/obitools/obiannotate/obiannotate.go b/pkg/obitools/obiannotate/obiannotate.go
index b57db51..aefab8a 100644
--- a/pkg/obitools/obiannotate/obiannotate.go
+++ b/pkg/obitools/obiannotate/obiannotate.go
@@ -47,7 +47,7 @@ func RenameAttributeWorker(toBeRenamed map[string]string) obiseq.SeqWorker {
 func AddTaxonAtRankWorker(taxonomy *obitax.Taxonomy, ranks ...string) obiseq.SeqWorker {
 	f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
 		for _, r := range ranks {
-			taxonomy.SetTaxonAtRank(s,r)
+			taxonomy.SetTaxonAtRank(s, r)
 		}
 		return s
 	}
@@ -55,6 +55,16 @@ func AddTaxonAtRankWorker(taxonomy *obitax.Taxonomy, ranks ...string) obiseq.Seq
 	return f
 }
 
+func AddSeqLengthWorker() obiseq.SeqWorker {
+	f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
+		s.SetAttribute("seq_length", s.Len())
+		return s
+	}
+
+	return f
+
+}
+
 func CLIAnnotationWorker() obiseq.SeqWorker {
 	var annotator obiseq.SeqWorker
 	annotator = nil
@@ -76,7 +86,12 @@ func CLIAnnotationWorker() obiseq.SeqWorker {
 
 	if CLIHasTaxonAtRank() {
 		taxo := obigrep.CLILoadSelectedTaxonomy()
-		w := AddTaxonAtRankWorker(taxo,CLITaxonAtRank()...)
+		w := AddTaxonAtRankWorker(taxo, CLITaxonAtRank()...)
+		annotator = annotator.ChainWorkers(w)
+	}
+
+	if CLIHasSetLengthFlag() {
+		w := AddSeqLengthWorker()
 		annotator = annotator.ChainWorkers(w)
 	}
 
diff --git a/pkg/obitools/obiannotate/options.go b/pkg/obitools/obiannotate/options.go
index eb691ab..9dbabf4 100644
--- a/pkg/obitools/obiannotate/options.go
+++ b/pkg/obitools/obiannotate/options.go
@@ -128,3 +128,7 @@ func CLIHasTaxonAtRank() bool {
 func CLITaxonAtRank() []string {
 	return _taxonAtRank
 }
+
+func CLIHasSetLengthFlag() bool {
+	return _setSeqLength
+}
\ No newline at end of file