X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/e473f1316af98ae33f3bea221d713049fbc8df81..0199de0f15752dd69086b1cf5401a13029f318ef:/gob.go

diff --git a/gob.go b/gob.go
index 2fb061c5b1..0bd1873961 100644
--- a/gob.go
+++ b/gob.go
@@ -1,44 +1,66 @@
-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+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
+	StartTag tagID
+	EndTag   tagID
+}
+
+type CompactSequence struct {
+	Name          string
+	TileSequences map[string][]tileLibRef
 }
 
 type TileVariant struct {
 	Tag      tagID
+	Ref      bool
 	Variant  tileVariantID
 	Blake2b  [blake2b.Size256]byte
 	Sequence []byte
 }
 
 type LibraryEntry struct {
-	TagSet         [][]byte
-	CompactGenomes []CompactGenome
-	TileVariants   []TileVariant
+	TagSet           [][]byte
+	CompactGenomes   []CompactGenome
+	CompactSequences []CompactSequence
+	TileVariants     []TileVariant
 }
 
-func ReadCompactGenomes(rdr io.Reader) ([]CompactGenome, error) {
+func ReadCompactGenomes(rdr io.Reader, gz bool) ([]CompactGenome, error) {
 	var ret []CompactGenome
-	err := DecodeLibrary(rdr, func(ent *LibraryEntry) error {
+	err := DecodeLibrary(rdr, gz, func(ent *LibraryEntry) error {
 		ret = append(ret, ent.CompactGenomes...)
 		return nil
 	})
 	return ret, err
 }
 
-func DecodeLibrary(rdr io.Reader, cb func(*LibraryEntry) error) error {
-	dec := gob.NewDecoder(bufio.NewReaderSize(rdr, 1<<26))
+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<<20))
+		if err != nil {
+			return err
+		}
+	}
+	dec := gob.NewDecoder(zrdr)
 	for err == nil {
 		var ent LibraryEntry
 		err = dec.Decode(&ent)
@@ -46,9 +68,8 @@ func DecodeLibrary(rdr io.Reader, cb func(*LibraryEntry) error) error {
 			err = cb(&ent)
 		}
 	}
-	if err == io.EOF {
-		return nil
-	} else {
+	if err != io.EOF {
 		return err
 	}
+	return zrdr.Close()
 }