Several bugs dicoverd during the doc writing

Release-notes.md

@@ -4,6 +4,15 @@
 
 ### Bug fixes
 
+- In `obipairing` correct the misspelling of the `obiparing_*` tags where the `i`
+  was missing to `obipairing_`.  
+
+- In `obigrep` the **-C** option that excludes sequences too abundant was not 
+  functional.
+
+- In `obitaxonomy` the **-l** option that lists all the taxonomic rank defined by
+  a taxonomy was not functional
+
 - The file type guesser was not using enough data to be able to correctly detect
   file format when sequences were too long in fastq and fasta or when lines were
   to long in CSV files. That's now corrected

cmd/obitools/obitaxonomy/main.go

@@ -4,9 +4,11 @@ import (
 	"os"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiitercsv"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicsv"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitaxonomy"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
@@ -37,13 +39,25 @@ func main() {
 	}
 
 	switch {
-	case obitaxonomy.CLIDownloadNCBI():
+	case obitaxonomy.CLIAskForRankList():
-		err := obitaxonomy.CLIDownloadNCBITaxdump()
+		newIter := obiitercsv.NewICSVRecord()
-		if err != nil {
+		newIter.Add(1)
-			log.Errorf("Cannot download NCBI taxonomy: %s", err.Error())
+		newIter.AppendField("rank")
-			os.Exit(1)
+		go func() {
-		}
+			ranks := obitax.DefaultTaxonomy().RankList()
+			data := make([]obiitercsv.CSVRecord, len(ranks))
 
+			for i, rank := range ranks {
+				record := make(obiitercsv.CSVRecord)
+				record["rank"] = rank
+				data[i] = record
+			}
+			newIter.Push(obiitercsv.MakeCSVRecordBatch(obitax.DefaultTaxonomy().Name(), 0, data))
+			newIter.Close()
+			newIter.Done()
+		}()
+		obicsv.CLICSVWriter(newIter, true)
+		obiutils.WaitForLastPipe()
 		os.Exit(0)
 
 	case obitaxonomy.CLIExtractTaxonomy():

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 = "2d52322"
+var _Commit = "03b5ce9"
 var _Version = "Release 4.4.0"
 
 // Version returns the version of the obitools package.

pkg/obitools/obigrep/options.go

@@ -223,7 +223,7 @@ func CLISequenceCountPredicate() obiseq.SequencePredicate {
 		return p
 	}
 
-	if _MaximumLength != int(2e9) {
+	if _MaximumCount != int(2e9) {
 		return obiseq.IsLessAbundantOrEqualTo(_MaximumCount)
 	}
 

pkg/obitools/obipairing/pairing.go

@@ -137,9 +137,9 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
 	annot := cons.Annotations()
 
 	if fastAlign {
-		annot["paring_fast_count"] = fastcount
+		annot["pairing_fast_count"] = fastcount
-		annot["paring_fast_score"] = math.Round(fastscore*1000) / 1000
+		annot["pairing_fast_score"] = math.Round(fastscore*1000) / 1000
-		annot["paring_fast_overlap"] = over
+		annot["pairing_fast_overlap"] = over
 	}
 
 	if aliLength >= minOverlap && identity >= minIdentity {

pkg/obitools/obitaxonomy/options.go

@@ -165,3 +165,7 @@ func CLIExtractTaxonomy() bool {
 func CLIAsNewick() bool {
 	return __newick__
 }
+
+func CLIAskForRankList() bool {
+	return __rank_list__
+}