func (d *DiversityFilter) findGenome(r *sam.Record, env *lmdb.Env, dbname string) (val []byte, err error) {
fn := func(txn *lmdb.Txn) error {
dbi, err := txn.OpenDBI(dbname, 0)
if err != nil {
return err
}
key := []byte(r.Ref.Name())
val, err = txn.Get(dbi, key)
val = bytes.ToUpper(val)
return err
}
err = env.View(fn)
return
}
func setVersionLMDB(env *lmdb.Env, metadbi lmdb.DBI, version int64) error {
return env.Update(func(tx *lmdb.Txn) error {
buf := new(bytes.Buffer)
err := binary.Write(buf, binary.LittleEndian, version)
if err != nil {
glog.Errorf("Couldn't convert version!")
return err
}
werr := tx.Put(metadbi, []byte("version"), buf.Bytes(), 0)
if werr != nil {
glog.Error("Couldn't write version!")
return werr
}
return nil
})
}
func createDBI(env *lmdb.Env, name string) error {
fn := func(txn *lmdb.Txn) error {
var dbi lmdb.DBI
var err error
var del bool = false
if dbi, err = txn.CreateDBI(name); err != nil {
return err
}
if err = txn.Drop(dbi, del); err != nil {
return err
}
return nil
}
err := env.Update(fn)
return err
}
func getAllCr(env *lmdb.Env, dbname string) chan KeyValue {
ch := make(chan KeyValue)
go func() {
defer close(ch)
fn := func(txn *lmdb.Txn) error {
dbi, err := txn.OpenDBI(dbname, 0)
if err != nil {
return err
}
cur, err := txn.OpenCursor(dbi)
if err != nil {
return err
}
for {
k, v, err := cur.Get(nil, nil, lmdb.Next)
if lmdb.IsNotFound(err) {
break
}
if err != nil {
return err
}
ch <- KeyValue{Key: k, Value: v}
}
return nil
}
err := env.View(fn)
if err != nil {
if *debug {
log.Panicln(err)
} else {
log.Fatalln(err)
}
}
}()
return ch
}
func getAllSNPs(env *lmdb.Env) chan SNPArr {
ch := make(chan SNPArr)
fn := func(tx *lmdb.Txn) error {
dbi, err := tx.OpenDBI("gene", 0)
if err != nil {
return err
}
cur, err := tx.OpenCursor(dbi)
if err != nil {
return err
}
defer cur.Close()
for {
k, v, err := cur.Get(nil, nil, lmdb.Next)
if lmdb.IsNotFound(err) {
return nil
} else if err != nil {
return err
}
arr := []pileup.SNP{}
if err := msgpack.Unmarshal(v, &arr); err != nil {
return err
}
ch <- SNPArr{Key: k, Arr: arr}
}
}
go func() {
defer close(ch)
env.View(fn)
}()
return ch
}