Merge branch 'master' into taxonomy

pkg/obitools/obiconvert/sequence_reader.go

@@ -99,6 +99,8 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 		opts = append(opts, obiformats.OptionsFastSeqHeaderParser(obiformats.ParseGuessedFastSeqHeader))
 	}
 
+	opts = append(opts, obiformats.OptionsReadQualities(obioptions.CLIReadQualities()))
+
 	nworkers := obioptions.CLIReadParallelWorkers()
 	if nworkers < 2 {
 		nworkers = 2

pkg/obitools/obipairing/pairing.go

@@ -9,6 +9,7 @@ import (
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func _Abs(x int) int {
@@ -112,7 +113,7 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
 	inplace bool, fastAlign, fastModeRel bool,
 	arenaAlign obialign.PEAlignArena, shifh_buff *map[int]int) *obiseq.BioSequence {
 
-	score, path, fastcount, over, fastscore := obialign.PEAlign(
+	isLeftAlign, score, path, fastcount, over, fastscore := obialign.PEAlign(
 		seqA, seqB,
 		gap, scale,
 		fastAlign, delta, fastModeRel,
@@ -143,19 +144,14 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
 	if aliLength >= minOverlap && identity >= minIdentity {
 		annot["mode"] = "alignment"
 		if withStats {
-			if left < 0 {
-				annot["seq_a_single"] = -left
+			if isLeftAlign {
 				annot["ali_dir"] = "left"
+				annot["seq_a_single"] = obiutils.Abs(left)
+				annot["seq_b_single"] = obiutils.Abs(right)
 			} else {
-				annot["seq_b_single"] = left
 				annot["ali_dir"] = "right"
-			}
-
-			if right < 0 {
-				right = -right
-				annot["seq_a_single"] = right
-			} else {
-				annot["seq_b_single"] = right
+				annot["seq_a_single"] = obiutils.Abs(right)
+				annot["seq_b_single"] = obiutils.Abs(left)
 			}
 		}
 		if inplace {

pkg/obitools/obitagpcr/options.go

@@ -9,7 +9,7 @@ import (
 var _reorientate = false
 
 func TagPCROptionSet(options *getoptions.GetOpt) {
-	options.BoolVar(&_reorientate, "reference-db", _reorientate,
+	options.BoolVar(&_reorientate, "reorientate", _reorientate,
 		options.Description("Reverse complemente reads if needed to store all the sequences in "+
 			"the same orientation respectively to forward and reverse primers"))
 

pkg/obitools/obitagpcr/pcrtag.go

@@ -64,7 +64,7 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
 	newIter := obiiter.MakeIBioSequence()
 	newIter.MarkAsPaired()
 
-	f := func(iterator obiiter.IBioSequence, wid int) {
+	f := func(iterator obiiter.IBioSequence) {
 		arena := obialign.MakePEAlignArena(150, 150)
 		shifts := make(map[int]int)
 
@@ -89,46 +89,51 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
 
 					forward_match := annot["obimultiplex_forward_match"].(string)
 					forward_mismatches := annot["obimultiplex_forward_error"].(int)
-					forward_tag := annot["obimultiplex_forward_tag"].(string)
 
 					reverse_match := annot["obimultiplex_reverse_match"].(string)
 					reverse_mismatches := annot["obimultiplex_reverse_error"].(int)
-					reverse_tag := annot["obimultiplex_reverse_tag"].(string)
 
 					sample := annot["sample"].(string)
 					experiment := annot["experiment"].(string)
 
 					aanot := A.Annotations()
+					banot := B.Annotations()
+
+					if value, ok := annot["obimultiplex_forward_tag"]; ok {
+						forward_tag := value.(string)
+						aanot["obimultiplex_forward_tag"] = forward_tag
+						banot["obimultiplex_forward_tag"] = forward_tag
+					}
+
+					if value, ok := annot["obimultiplex_reverse_tag"]; ok {
+						reverse_tag := value.(string)
+						aanot["obimultiplex_reverse_tag"] = reverse_tag
+						banot["obimultiplex_reverse_tag"] = reverse_tag
+					}
+
 					aanot["obimultiplex_direction"] = direction
 
 					aanot["obimultiplex_forward_match"] = forward_match
 					aanot["obimultiplex_forward_mismatches"] = forward_mismatches
-					aanot["obimultiplex_forward_tag"] = forward_tag
 
 					aanot["obimultiplex_reverse_match"] = reverse_match
 					aanot["obimultiplex_reverse_mismatches"] = reverse_mismatches
-					aanot["obimultiplex_reverse_tag"] = reverse_tag
 
 					aanot["sample"] = sample
 					aanot["experiment"] = experiment
 
-					banot := B.Annotations()
 					banot["obimultiplex_direction"] = direction
 
 					banot["obimultiplex_forward_match"] = forward_match
 					banot["obimultiplex_forward_mismatches"] = forward_mismatches
-					banot["obimultiplex_forward_tag"] = forward_tag
 
 					banot["obimultiplex_reverse_match"] = reverse_match
 					banot["obimultiplex_reverse_mismatches"] = reverse_mismatches
-					banot["obimultiplex_reverse_tag"] = reverse_tag
 
 					banot["sample"] = sample
 					banot["experiment"] = experiment
 
 					if CLIReorientate() && direction == "reverse" {
-						B.ReverseComplement(true)
-						A.ReverseComplement(true)
 						B.PairTo(A)
 						batch.Slice()[i] = B
 					}
@@ -162,9 +167,9 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
 
 	newIter.Add(nworkers)
 	for i := 1; i < nworkers; i++ {
-		go f(iterator.Split(), i)
+		go f(iterator.Split())
 	}
-	go f(iterator, 0)
+	go f(iterator)
 
 	go func() {
 		newIter.WaitAndClose()