From 371e702423be39f019f792c427f12754eb9263dc Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Thu, 18 Dec 2025 14:10:56 +0100
Subject: [PATCH] obiannotate --cut bug

---
 pkg/obitools/obiannotate/obiannotate.go | 10 +++++-----
 pkg/obitools/obiannotate/options.go     | 14 ++++++++++++--
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/pkg/obitools/obiannotate/obiannotate.go b/pkg/obitools/obiannotate/obiannotate.go
index 8c410d9..8ab5fce 100644
--- a/pkg/obitools/obiannotate/obiannotate.go
+++ b/pkg/obitools/obiannotate/obiannotate.go
@@ -134,12 +134,12 @@ func CutSequenceWorker(from, to int, breakOnError bool) obiseq.SeqWorker {
 			t = to
 		}
 
-		if from < 0 {
-			from = 0
+		if f < 0 {
+			f = 0
 		}
 
-		if to >= s.Len() {
-			to = s.Len()
+		if t >= s.Len() {
+			t = s.Len()
 		}
 
 		rep, err := s.Subsequence(f, t, false)
@@ -147,7 +147,7 @@ func CutSequenceWorker(from, to int, breakOnError bool) obiseq.SeqWorker {
 			if breakOnError {
 				log.Fatalf("Cannot cut sequence %s (%v)", s.Id(), err)
 			} else {
-				err = fmt.Errorf("Cannot cut sequence %s (%v), sequence discarded", s.Id(), err)
+				err = fmt.Errorf("cannot cut sequence %s (%v), sequence discarded", s.Id(), err)
 			}
 		}
 		return obiseq.BioSequenceSlice{rep}, err
diff --git a/pkg/obitools/obiannotate/options.go b/pkg/obitools/obiannotate/options.go
index 437e124..c7b3179 100644
--- a/pkg/obitools/obiannotate/options.go
+++ b/pkg/obitools/obiannotate/options.go
@@ -1,6 +1,7 @@
 package obiannotate
 
 import (
+	"math"
 	"os"
 	"strconv"
 	"strings"
@@ -266,6 +267,7 @@ func CLICut() (int, int) {
 		return 0, 0
 	}
 	values := strings.Split(_cut, ":")
+	log.Warnf("values: %v (%d-%d)", values, len(values), len(values[1]))
 
 	if len(values) != 2 {
 		log.Fatalf("Invalid cut value %s. value should be of the form start:end", _cut)
@@ -274,12 +276,20 @@ func CLICut() (int, int) {
 	start, err := strconv.Atoi(values[0])
 
 	if err != nil {
-		log.Fatalf("Invalid cut value %s. value %s should be an integer", _cut, values[0])
+		if len(values[0]) == 0 {
+			start = 1
+		} else {
+			log.Fatalf("Invalid start cut value %s. value %s should be an integer", _cut, values[0])
+		}
 	}
 	end, err := strconv.Atoi(values[1])
 
 	if err != nil {
-		log.Fatalf("Invalid cut value %s. value %s should be an integer", _cut, values[1])
+		if len(values[1]) == 0 {
+			end = math.MaxInt
+		} else {
+			log.Fatalf("Invalid end cut value %s. value %s should be an integer", _cut, values[1])
+		}
 	}
 
 	return start, end