First functional version of a blackboard and a blackboard based obicount

pkg/obiblackboard/count_sequences.go

@@ -0,0 +1,50 @@
+package obiblackboard
+
+import (
+	"sync"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+)
+
+type SequenceCounter struct {
+	Variants    int
+	Reads       int
+	Nucleotides int
+	Runner      DoTask
+}
+
+func CountSequenceAggregator(target string) *SequenceCounter {
+	cc := &SequenceCounter{
+		Variants:    0,
+		Reads:       0,
+		Nucleotides: 0,
+		Runner:      nil,
+	}
+
+	mutex := sync.Mutex{}
+
+	runner := func(bb *Blackboard, task *Task) *Task {
+		body := task.Body.(obiiter.BioSequenceBatch)
+
+		mutex.Lock()
+		cc.Variants += body.Len()
+		cc.Reads += body.Slice().Count()
+		cc.Nucleotides += body.Slice().Size()
+		mutex.Unlock()
+
+		nt := task.GetNext(target, true, false)
+		return nt
+	}
+
+	cc.Runner = runner
+	return cc
+}
+
+func RecycleSequences(rescycleSequence bool, target string) DoTask {
+	return func(bb *Blackboard, task *Task) *Task {
+		body := task.Body.(obiiter.BioSequenceBatch)
+		// log.Warningf("With priority %d, Recycling %s[%d]", task.Priority, body.Source(), body.Order())
+		body.Recycle(rescycleSequence)
+		return task.GetNext(target, false, false)
+	}
+}