Gzip gob files.

[lightning.git] / stats.go

diff --git a/stats.go b/stats.go
index 8da2a69ad75afb3ebfe72e28aa2f3d59c80bd792..460eef47fb29b865b1c4dd05158b96a80ad0a1dc 100644 (file)
--- a/stats.go
+++ b/stats.go
@@ -2,7 +2,6 @@ package main
 
 import (
        "bufio"
-       "encoding/gob"
        "encoding/json"
        "errors"
        "flag"
@@ -12,6 +11,7 @@ import (
        "net/http"
        _ "net/http/pprof"
        "os"
+       "strings"
 
        "git.arvados.org/arvados.git/sdk/go/arvados"
        log "github.com/sirupsen/logrus"
@@ -101,7 +101,7 @@ func (cmd *statscmd) RunCommand(prog string, args []string, stdin io.Reader, std
        }
 
        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 +116,7 @@ func (cmd *statscmd) RunCommand(prog string, args []string, stdin io.Reader, std
        return 0
 }
 
-func (cmd *statscmd) 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 +131,7 @@ func (cmd *statscmd) 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 +178,10 @@ func (cmd *statscmd) 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 {