package lightning import ( "bufio" "encoding/gob" "io" "io/ioutil" _ "net/http/pprof" "github.com/klauspost/pgzip" "golang.org/x/crypto/blake2b" ) type CompactGenome struct { Name string Variants []tileVariantID } type CompactSequence struct { Name string TileSequences map[string][]tileLibRef } type TileVariant struct { Tag tagID Variant tileVariantID Blake2b [blake2b.Size256]byte Sequence []byte } type LibraryEntry struct { TagSet [][]byte CompactGenomes []CompactGenome CompactSequences []CompactSequence TileVariants []TileVariant } func ReadCompactGenomes(rdr io.Reader, gz bool) ([]CompactGenome, error) { var ret []CompactGenome err := DecodeLibrary(rdr, gz, func(ent *LibraryEntry) error { ret = append(ret, ent.CompactGenomes...) return nil }) return ret, err } func DecodeLibrary(rdr io.Reader, gz bool, cb func(*LibraryEntry) error) error { zrdr := ioutil.NopCloser(rdr) var err error if gz { zrdr, err = pgzip.NewReader(bufio.NewReaderSize(rdr, 1<<26)) if err != nil { return err } } dec := gob.NewDecoder(zrdr) for err == nil { var ent LibraryEntry err = dec.Decode(&ent) if err == nil { err = cb(&ent) } } if err != io.EOF { return err } return zrdr.Close() }