import (
"bufio"
- "encoding/gob"
"encoding/json"
"errors"
"flag"
"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 {
}
bufw := bufio.NewWriter(output)
- err = cmd.doStats(input, bufw)
+ err = cmd.doStats(input, strings.HasSuffix(*inputFilename, ".gz"), bufw)
if err != nil {
return 1
}
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
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 {
}
ret.CalledBases = append(ret.CalledBases, calledBases)
}
+ return nil
+ })
+ if err != nil {
+ return err
}
for id, p := range tagPlacements {
for len(ret.TagsPlacedNTimes) <= p {