From 2452aef7a9618a4ae8a4edfa1b31942a75263ccd Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Wed, 29 Jan 2025 21:35:28 +0100
Subject: [PATCH] patch multiple -Z options

---
 pkg/obioptions/options.go          |  4 ----
 pkg/obioptions/version.go          |  2 +-
 pkg/obitax/default_taxonomy.go     | 19 +++++++++++++------
 pkg/obitax/taxonset.go             | 26 ++++++++++++++++++++++++++
 pkg/obitools/obiconvert/options.go |  6 ++++--
 5 files changed, 44 insertions(+), 13 deletions(-)

diff --git a/pkg/obioptions/options.go b/pkg/obioptions/options.go
index 50d8824..68daa57 100644
--- a/pkg/obioptions/options.go
+++ b/pkg/obioptions/options.go
@@ -66,10 +66,6 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 		options.GetEnv("OBISOLEXA"),
 		options.Description("Decodes quality string according to the Solexa specification."))
 
-	options.BoolVar(obidefault.CompressedPtr(), "compressed", obidefault.CompressOutput(),
-		options.Alias("Z"),
-		options.Description("Compress all the result using gzip"))
-
 	for _, o := range optionset {
 		o(options)
 	}
diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go
index 67fc46e..6115614 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 = "8a28c9a"
+var _Commit = "3379545"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.
diff --git a/pkg/obitax/default_taxonomy.go b/pkg/obitax/default_taxonomy.go
index df7d886..219d321 100644
--- a/pkg/obitax/default_taxonomy.go
+++ b/pkg/obitax/default_taxonomy.go
@@ -1,11 +1,14 @@
 package obitax
 
 import (
+	"sync"
+
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	log "github.com/sirupsen/logrus"
 )
 
 var __defaut_taxonomy__ *Taxonomy
+var __defaut_taxonomy_mutex__ sync.Mutex
 
 func (taxonomy *Taxonomy) SetAsDefault() {
 	log.Infof("Set as default taxonomy %s", taxonomy.Name())
@@ -32,14 +35,18 @@ func DefaultTaxonomy() *Taxonomy {
 	var err error
 	if __defaut_taxonomy__ == nil {
 		if obidefault.HasSelectedTaxonomy() {
-			__defaut_taxonomy__, err = LoadTaxonomy(
-				obidefault.SelectedTaxonomy(),
-				!obidefault.AreAlternativeNamesSelected(),
-			)
+			__defaut_taxonomy_mutex__.Lock()
+			defer __defaut_taxonomy_mutex__.Unlock()
+			if __defaut_taxonomy__ == nil {
+				__defaut_taxonomy__, err = LoadTaxonomy(
+					obidefault.SelectedTaxonomy(),
+					!obidefault.AreAlternativeNamesSelected(),
+				)
 
-			if err != nil {
-				log.Fatalf("Cannot load default taxonomy: %v", err)
+				if err != nil {
+					log.Fatalf("Cannot load default taxonomy: %v", err)
 
+				}
 			}
 		}
 	}
diff --git a/pkg/obitax/taxonset.go b/pkg/obitax/taxonset.go
index 9e6f7c2..9d2da84 100644
--- a/pkg/obitax/taxonset.go
+++ b/pkg/obitax/taxonset.go
@@ -196,3 +196,29 @@ func (set *TaxonSet) Contains(id *string) bool {
 	node := set.Get(id)
 	return node != nil
 }
+
+func (set *TaxonSet) Sort() *TaxonSlice {
+	if set == nil {
+		return nil
+	}
+
+	taxonomy := set.Taxonomy()
+	taxa := taxonomy.NewTaxonSlice(0, set.Len())
+	parent := make(map[*TaxNode]bool, set.Len())
+
+	pushed := true
+
+	for pushed {
+		pushed = false
+		for _, node := range set.set {
+			if !parent[node] && (parent[set.Get(node.parent).Node] ||
+				!set.Contains(node.parent)) {
+				pushed = true
+				taxa.slice = append(taxa.slice, node)
+				parent[node] = true
+			}
+		}
+	}
+
+	return taxa
+}
diff --git a/pkg/obitools/obiconvert/options.go b/pkg/obitools/obiconvert/options.go
index 6893432..22684df 100644
--- a/pkg/obitools/obiconvert/options.go
+++ b/pkg/obitools/obiconvert/options.go
@@ -3,6 +3,7 @@ package obiconvert
 import (
 	"os"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	log "github.com/sirupsen/logrus"
 
@@ -76,9 +77,10 @@ func OutputModeOptionSet(options *getoptions.GetOpt, compressed bool) {
 		options.Description("Disable the progress bar printing"))
 
 	if compressed {
-		options.BoolVar(&__compressed__, "compress", false,
+		options.BoolVar(obidefault.CompressedPtr(), "compressed", obidefault.CompressOutput(),
 			options.Alias("Z"),
-			options.Description("Output is compressed"))
+			options.Description("Compress all the result using gzip"))
+
 	}
 
 	options.StringVar(&__output_file_name__, "out", __output_file_name__,