From 6141d404cdf9c54b385568cf4c2166c022ed62a2 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Wed, 22 Nov 2023 14:51:56 +0100
Subject: [PATCH] patch a bug related to --count option of obicsv

Former-commit-id: e19e8cc12a99216d24c5e0c5350c273202d84de4
---
 pkg/obitools/obicsv/options.go | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/pkg/obitools/obicsv/options.go b/pkg/obitools/obicsv/options.go
index 598398e..aeedab1 100644
--- a/pkg/obitools/obicsv/options.go
+++ b/pkg/obitools/obicsv/options.go
@@ -77,9 +77,24 @@ func CLIPrintSequence() bool {
 }
 
 func CLIPrintCount() bool {
+	if i := obiutils.LookFor(_keepOnly, "count"); i >= 0 {
+		_keepOnly = obiutils.RemoveIndex(_keepOnly, i)
+		_outputCount = true
+	}
+
 	return _outputCount
 }
 func CLIPrintTaxon() bool {
+	if i := obiutils.LookFor(_keepOnly, "taxid"); i >= 0 {
+		_keepOnly = obiutils.RemoveIndex(_keepOnly, i)
+		_outputTaxon = true
+	}
+
+	if i := obiutils.LookFor(_keepOnly, "scientific_name"); i >= 0 {
+		_keepOnly = obiutils.RemoveIndex(_keepOnly, i)
+		_outputTaxon = true
+	}
+
 	return _outputTaxon
 }
 func CLIPrintQuality() bool {