From ff51cc7393205856773da2a2f0ab787f3a0bfc1b Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Wed, 22 Nov 2023 07:05:22 +0100
Subject: [PATCH] Adds a --transpose option to obimatrix

Former-commit-id: b2ee47c15441dca971b20f583003a3788a96da23
---
 pkg/obitools/obimatrix/obimatrix.go | 4 +++-
 pkg/obitools/obimatrix/options.go   | 8 ++++++++
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/pkg/obitools/obimatrix/obimatrix.go b/pkg/obitools/obimatrix/obimatrix.go
index 4b5ee6b..831d5f8 100644
--- a/pkg/obitools/obimatrix/obimatrix.go
+++ b/pkg/obitools/obimatrix/obimatrix.go
@@ -137,7 +137,9 @@ func CLIWriteCSVToStdout(matrix *MatrixData) {
 	navalue := CLINaValue()
 	csvwriter := csv.NewWriter(os.Stdout)
 
-	matrix = matrix.TransposeMatrixData()
+	if CLITranspose() {
+		matrix = matrix.TransposeMatrixData()
+	}
 
 	samples := obiutils.NewSet[string]()
 
diff --git a/pkg/obitools/obimatrix/options.go b/pkg/obitools/obimatrix/options.go
index e91ccb3..da4c766 100644
--- a/pkg/obitools/obimatrix/options.go
+++ b/pkg/obitools/obimatrix/options.go
@@ -10,6 +10,7 @@ import (
 )
 
 var __threeColumns__ = false
+var __transpose__ = true
 var __mapAttribute__ = "merged_sample"
 var __valueName__ = "count"
 var __sampleName__ = "sample"
@@ -19,6 +20,9 @@ func MatrixOptionSet(options *getoptions.GetOpt) {
 	options.BoolVar(&__threeColumns__, "three-columns", false,
 		options.Description("Printouts the matrix in tree column format."))
 
+	options.BoolVar(&__transpose__, "transpose", __transpose__,
+		options.Description("Printouts the transposed matrix."))
+
 	options.StringVar(&__mapAttribute__, "map", __mapAttribute__,
 		options.Description("Which attribute is usd to produce th matrix."))
 
@@ -60,3 +64,7 @@ func CLINaValue() string {
 func CLIMapAttribute() string {
 	return __mapAttribute__
 }
+
+func CLITranspose() bool {
+	return __transpose__
+}