gob.go

   1 package main
   2
   3 import (
   4         "bufio"
   5         "encoding/gob"
   6         "io"
   7         "io/ioutil"
   8         _ "net/http/pprof"
   9
  10         "github.com/klauspost/pgzip"
  11         "golang.org/x/crypto/blake2b"
  12 )
  13
  14 type CompactGenome struct {
  15         Name     string
  16         Variants []tileVariantID
  17 }
  18
  19 type CompactSequence struct {
  20         Name          string
  21         TileSequences map[string][]tileLibRef
  22 }
  23
  24 type TileVariant struct {
  25         Tag      tagID
  26         Variant  tileVariantID
  27         Blake2b  [blake2b.Size256]byte
  28         Sequence []byte
  29 }
  30
  31 type LibraryEntry struct {
  32         TagSet           [][]byte
  33         CompactGenomes   []CompactGenome
  34         CompactSequences []CompactSequence
  35         TileVariants     []TileVariant
  36 }
  37
  38 func ReadCompactGenomes(rdr io.Reader, gz bool) ([]CompactGenome, error) {
  39         var ret []CompactGenome
  40         err := DecodeLibrary(rdr, gz, func(ent *LibraryEntry) error {
  41                 ret = append(ret, ent.CompactGenomes...)
  42                 return nil
  43         })
  44         return ret, err
  45 }
  46
  47 func DecodeLibrary(rdr io.Reader, gz bool, cb func(*LibraryEntry) error) error {
  48         zrdr := ioutil.NopCloser(rdr)
  49         var err error
  50         if gz {
  51                 zrdr, err = pgzip.NewReader(bufio.NewReaderSize(rdr, 1<<26))
  52                 if err != nil {
  53                         return err
  54                 }
  55         }
  56         dec := gob.NewDecoder(zrdr)
  57         for err == nil {
  58                 var ent LibraryEntry
  59                 err = dec.Decode(&ent)
  60                 if err == nil {
  61                         err = cb(&ent)
  62                 }
  63         }
  64         if err != io.EOF {
  65                 return err
  66         }
  67         return zrdr.Close()
  68 }