Patch a bug on compressed output

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 = "b9bee5f"
+var _Commit = "ceca339"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.

pkg/obitax/csvtaxdump_write.go

@@ -1 +1,38 @@
 package obitax
+
+import (
+	"strings"
+
+	"github.com/TuftsBCB/io/newick"
+)
+
+func (taxonomy *Taxonomy) Newick() string {
+	if taxonomy == nil {
+		return ""
+	}
+
+	iterator := taxonomy.AsTaxonSet().Sort().Iterator()
+
+	nodes := make(map[*string]*newick.Tree, taxonomy.Len())
+	trees := make([]*newick.Tree, 0)
+
+	for iterator.Next() {
+		taxon := iterator.Get()
+		tree := &newick.Tree{Label: taxon.String()}
+		nodes[taxon.Node.id] = tree
+		if parent, ok := nodes[taxon.Parent().Node.id]; ok {
+			parent.Children = append(parent.Children, *tree)
+		} else {
+			trees = append(trees, tree)
+		}
+	}
+
+	rep := strings.Builder{}
+
+	for _, tree := range trees {
+		rep.WriteString(tree.String())
+		rep.WriteString("\n")
+	}
+
+	return rep.String()
+}

pkg/obitax/newick_write.go

@@ -0,0 +1 @@
+package obitax

pkg/obitools/obiconvert/options.go

@@ -163,10 +163,6 @@ func CLIOutputFormat() string {
 	}
 }
 
-func CLICompressed() bool {
-	return __compressed__
-}
-
 func CLISkipEmpty() bool {
 	return __skip_empty__
 }

pkg/obitools/obiconvert/sequence_writer.go

@@ -58,7 +58,7 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 	opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
 	opts = append(opts, obiformats.OptionsBatchSize(obidefault.BatchSize()))
 
-	opts = append(opts, obiformats.OptionsCompressed(CLICompressed()))
+	opts = append(opts, obiformats.OptionsCompressed(obidefault.CompressOutput()))
 
 	var err error
 

pkg/obitools/obidistribute/distribute.go

@@ -33,7 +33,7 @@ func CLIDistributeSequence(sequences obiiter.IBioSequence) {
 	opts = append(opts, obiformats.OptionsParallelWorkers(nworkers),
 		obiformats.OptionsBatchSize(obidefault.BatchSize()),
 		obiformats.OptionsAppendFile(CLIAppendSequences()),
-		obiformats.OptionsCompressed(obiconvert.CLICompressed()))
+		obiformats.OptionsCompressed(obidefault.CompressOutput()))
 
 	var formater obiformats.SequenceBatchWriterToFile