Add the --number option to obiannotate

pkg/obiiter/numbering.go

@@ -0,0 +1,62 @@
+package obiiter
+
+import (
+	"sync"
+	"sync/atomic"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
+)
+
+func (iter IBioSequence) NumberSequences(start int, forceReordering bool) IBioSequence {
+
+	next_first := &atomic.Int64{}
+	next_first.Store(int64(start))
+	lock := &sync.Mutex{}
+
+	w := obidefault.ParallelWorkers()
+	if forceReordering {
+		iter = iter.SortBatches()
+		w = 1
+	}
+
+	newIter := MakeIBioSequence()
+	newIter.Add(w)
+
+	is_paired := false
+
+	if iter.IsPaired() {
+		is_paired = true
+		newIter.MarkAsPaired()
+	}
+
+	number := func(iter IBioSequence) {
+		for iter.Next() {
+			batch := iter.Get()
+			seqs := batch.Slice()
+			lock.Lock()
+			start := int(next_first.Load())
+			next_first.Store(int64(start + len(seqs)))
+			lock.Unlock()
+			for i, seq := range seqs {
+				num := start + i
+				seq.SetAttribute("seq_number", num)
+				if is_paired {
+					seq.PairedWith().SetAttribute("seq_number", num)
+				}
+			}
+			newIter.Push(batch)
+		}
+		newIter.Done()
+	}
+
+	go func() {
+		newIter.WaitAndClose()
+	}()
+
+	for i := 1; i < w; i++ {
+		go number(iter.Split())
+	}
+	go number(iter)
+
+	return newIter
+}