X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/4f4ea734de16bfd4515f12b95f4bf0f282db8def..129f23a9792303778d5e4d7447bfaf9f19e2d2ee:/stats.go

diff --git a/stats.go b/stats.go
index a02fef701d..69e66da9a7 100644
--- a/stats.go
+++ b/stats.go
@@ -1,8 +1,11 @@
-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
 
 import (
 	"bufio"
-	"encoding/gob"
 	"encoding/json"
 	"errors"
 	"flag"
@@ -12,16 +15,17 @@ import (
 	"net/http"
 	_ "net/http/pprof"
 	"os"
+	"strings"
 
 	"git.arvados.org/arvados.git/sdk/go/arvados"
 	log "github.com/sirupsen/logrus"
 )
 
-type stats struct {
+type statscmd struct {
 	debugUnplaced bool
 }
 
-func (cmd *stats) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
+func (cmd *statscmd) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
 	var err error
 	defer func() {
 		if err != nil {
@@ -101,7 +105,7 @@ func (cmd *stats) RunCommand(prog string, args []string, stdin io.Reader, stdout
 	}
 
 	bufw := bufio.NewWriter(output)
-	err = cmd.doStats(input, bufw)
+	err = cmd.doStats(input, strings.HasSuffix(*inputFilename, ".gz"), bufw)
 	if err != nil {
 		return 1
 	}
@@ -116,7 +120,7 @@ func (cmd *stats) RunCommand(prog string, args []string, stdin io.Reader, stdout
 	return 0
 }
 
-func (cmd *stats) doStats(input io.Reader, output io.Writer) error {
+func (cmd *statscmd) doStats(input io.Reader, gz bool, output io.Writer) error {
 	var ret struct {
 		Genomes          int
 		CalledBases      []int64
@@ -131,15 +135,7 @@ func (cmd *stats) doStats(input io.Reader, output io.Writer) error {
 	var tagSet [][]byte
 	var tagPlacements []int
 	tileVariantCalls := map[tileLibRef]int{}
-	dec := gob.NewDecoder(bufio.NewReaderSize(input, 1<<26))
-	for {
-		var ent LibraryEntry
-		err := dec.Decode(&ent)
-		if err == io.EOF {
-			break
-		} else if err != nil {
-			return fmt.Errorf("gob decode: %w", err)
-		}
+	err := DecodeLibrary(input, gz, func(ent *LibraryEntry) error {
 		ret.Genomes += len(ent.CompactGenomes)
 		ret.TileVariants += len(ent.TileVariants)
 		if len(ent.TagSet) > 0 {
@@ -186,6 +182,10 @@ func (cmd *stats) doStats(input io.Reader, output io.Writer) error {
 			}
 			ret.CalledBases = append(ret.CalledBases, calledBases)
 		}
+		return nil
+	})
+	if err != nil {
+		return err
 	}
 	for id, p := range tagPlacements {
 		for len(ret.TagsPlacedNTimes) <= p {