From ed28d3fb5bd0830378b8bd498037669229b04cc2 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Mon, 7 Jul 2025 15:35:26 +0200
Subject: [PATCH] Adds a --u-to-t option

---
 pkg/obioptions/version.go                  | 2 +-
 pkg/obitools/obiconvert/options.go         | 9 +++++++++
 pkg/obitools/obiconvert/sequence_reader.go | 1 +
 3 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go
index b451e4a..605ac73 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 = "235a7e2"
+var _Commit = "43b2855"
 var _Version = "Release 4.4.0"
 
 // Version returns the version of the obitools package.
diff --git a/pkg/obitools/obiconvert/options.go b/pkg/obitools/obiconvert/options.go
index 47b0a98..3776bdf 100644
--- a/pkg/obitools/obiconvert/options.go
+++ b/pkg/obitools/obiconvert/options.go
@@ -40,6 +40,8 @@ var __paired_file_name__ = ""
 
 var __full_file_batch__ = false
 
+var __U_to_T = false
+
 func InputOptionSet(options *getoptions.GetOpt) {
 	// options.IntVar(&__skipped_entries__, "skip", __skipped_entries__,
 	// 	options.Description("The N first sequence records of the file are discarded from the analysis and not reported to the output file."))
@@ -74,6 +76,9 @@ func InputOptionSet(options *getoptions.GetOpt) {
 		options.Description("When several input files are provided, "+
 			"indicates that there is no order among them."))
 
+	options.BoolVar(&__U_to_T, "u-to-t", __U_to_T,
+		options.Description("Convert Uracil to Thymine."))
+
 }
 
 func OutputModeOptionSet(options *getoptions.GetOpt, compressed bool) {
@@ -239,6 +244,10 @@ func CLIPairedFileName() string {
 	return __paired_file_name__
 }
 
+func CLIUtoT() bool {
+	return __U_to_T
+}
+
 func SetFullFileBatch() {
 	__full_file_batch__ = true
 }
diff --git a/pkg/obitools/obiconvert/sequence_reader.go b/pkg/obitools/obiconvert/sequence_reader.go
index 48b8306..bc2759c 100644
--- a/pkg/obitools/obiconvert/sequence_reader.go
+++ b/pkg/obitools/obiconvert/sequence_reader.go
@@ -112,6 +112,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 	opts = append(opts, obiformats.OptionsBatchSize(obidefault.BatchSize()))
 
 	opts = append(opts, obiformats.OptionsFullFileBatch(FullFileBatch()))
+	opts = append(opts, obiformats.OptionsUtoT(CLIUtoT()))
 
 	if len(filenames) == 0 {
 		log.Printf("Reading sequences from stdin in %s\n", CLIInputFormat())