From 4df99cec5b7628a0a35c5e5fd855c2a8c0fde22c Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Tue, 23 Aug 2022 11:10:04 +0200
Subject: [PATCH] Chang log package

---
 pkg/obitools/obiclean/graph.go  |  3 ++-
 pkg/obitools/obigrep/options.go | 19 ++++++++++++-------
 2 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/pkg/obitools/obiclean/graph.go b/pkg/obitools/obiclean/graph.go
index b0ada8f..fe0ad87 100644
--- a/pkg/obitools/obiclean/graph.go
+++ b/pkg/obitools/obiclean/graph.go
@@ -3,7 +3,6 @@ package obiclean
 import (
 	"bytes"
 	"fmt"
-	"log"
 	"math"
 	"os"
 	"path"
@@ -11,6 +10,8 @@ import (
 	"sync"
 	"text/template"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
 	"github.com/schollz/progressbar/v3"
 )
diff --git a/pkg/obitools/obigrep/options.go b/pkg/obitools/obigrep/options.go
index 7d2b695..aab5594 100644
--- a/pkg/obitools/obigrep/options.go
+++ b/pkg/obitools/obigrep/options.go
@@ -1,9 +1,10 @@
 package obigrep
 
 import (
-	"log"
 	"strings"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats/ncbitaxdump"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
@@ -177,6 +178,10 @@ func CLIMaxSequenceCount() int {
 	return _MaximumCount
 }
 
+func CLIRequiredRanks() []string {
+	return _RequiredRanks
+}
+
 func CLISequenceCountPredicate() obiseq.SequencePredicate {
 	if _MinimumCount > 1 {
 		p := obiseq.IsMoreAbundantOrEqualTo(_MinimumCount)
@@ -222,10 +227,10 @@ func CLIRestrictTaxonomyPredicate() obiseq.SequencePredicate {
 
 	if len(_BelongTaxa) > 0 {
 		taxonomy := CLILoadSelectedTaxonomy()
-		p := obitax.IsSubCladeOf(*taxonomy, _BelongTaxa[0])
+		p := taxonomy.IsSubCladeOf(_BelongTaxa[0])
 
 		for _, taxid := range _BelongTaxa[1:] {
-			p = p.Or(obitax.IsSubCladeOf(*taxonomy, taxid))
+			p = p.Or(taxonomy.IsSubCladeOf(taxid))
 		}
 
 		return p
@@ -238,10 +243,10 @@ func CLIAvoidTaxonomyPredicate() obiseq.SequencePredicate {
 
 	if len(_NotBelongTaxa) > 0 {
 		taxonomy := CLILoadSelectedTaxonomy()
-		p := obitax.IsSubCladeOf(*taxonomy, _NotBelongTaxa[0])
+		p := taxonomy.IsSubCladeOf(_NotBelongTaxa[0])
 
 		for _, taxid := range _NotBelongTaxa[1:] {
-			p = p.Or(obitax.IsSubCladeOf(*taxonomy, taxid))
+			p = p.Or(taxonomy.IsSubCladeOf(taxid))
 		}
 
 		return p.Not()
@@ -254,10 +259,10 @@ func CLIHasRankDefinedPredicate() obiseq.SequencePredicate {
 
 	if len(_RequiredRanks) > 0 {
 		taxonomy := CLILoadSelectedTaxonomy()
-		p := obitax.HasRankDefined(*taxonomy, _RequiredRanks[0])
+		p := taxonomy.HasRequiredRank(_RequiredRanks[0])
 
 		for _, rank := range _RequiredRanks[1:] {
-			p = p.And(obitax.HasRankDefined(*taxonomy, rank))
+			p = p.And(taxonomy.HasRequiredRank(rank))
 		}
 
 		return p