func (d *DiversityFilter) filter(buf []*sam.Record, acc string, genome []byte) (out []*sam.Record, acc1 string, genome1 []byte) {
fn := func(txn *lmdb.Txn) error {
dbi, err := txn.OpenDBI("read", 0)
if err != nil {
return err
}
for _, r := range buf {
key := []byte(r.Name)
val, err := txn.Get(dbi, key)
if err != nil {
if lmdb.IsNotFound(err) {
val, err = r.MarshalText()
if err != nil {
return err
}
err = txn.Put(dbi, key, val, 0)
if err != nil {
return err
}
} else {
return err
}
} else {
var mate *sam.Record = &sam.Record{}
err := mate.UnmarshalText(val)
raiseError(err)
if r.Ref.Name() == mate.Ref.Name() {
if acc != r.Ref.Name() {
genome, err = d.findGenome(r, d.featureDB, "fna")
raiseError(err)
acc = r.Ref.Name()
if *debug {
log.Println(acc)
}
}
diff1, len1 := d.Diff(r, genome)
diff2, len2 := d.Diff(mate, genome)
if len1 > 0 && len2 > 0 && float64(diff1+diff2)/float64(len1+len2) <= d.Cutoff {
out = append(out, r)
out = append(out, mate)
} else {
if *debug {
log.Printf("%d, %d, %d, %d\n", diff1, diff2, len1, len2)
}
}
}
txn.Del(dbi, key, val)
}
}
return nil
}
retry:
err := d.db.Update(fn)
if lmdb.IsMapFull(err) {
d.sizeDB *= 2
err = d.db.SetMapSize(d.sizeDB)
raiseError(err)
goto retry
}
raiseError(err)
genome1 = genome
acc1 = acc
return
}
