stats.go

   1 package lightning
   2
   3 import (
   4         "bufio"
   5         "encoding/json"
   6         "errors"
   7         "flag"
   8         "fmt"
   9         "io"
  10         "io/ioutil"
  11         "net/http"
  12         _ "net/http/pprof"
  13         "os"
  14         "strings"
  15
  16         "git.arvados.org/arvados.git/sdk/go/arvados"
  17         log "github.com/sirupsen/logrus"
  18 )
  19
  20 type statscmd struct {
  21         debugUnplaced bool
  22 }
  23
  24 func (cmd *statscmd) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  25         var err error
  26         defer func() {
  27                 if err != nil {
  28                         fmt.Fprintf(stderr, "%s\n", err)
  29                 }
  30         }()
  31         flags := flag.NewFlagSet("", flag.ContinueOnError)
  32         flags.SetOutput(stderr)
  33         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  34         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  35         projectUUID := flags.String("project", "", "project `UUID` for output data")
  36         priority := flags.Int("priority", 500, "container request priority")
  37         inputFilename := flags.String("i", "-", "input `file`")
  38         outputFilename := flags.String("o", "-", "output `file`")
  39         flags.BoolVar(&cmd.debugUnplaced, "debug-unplaced", false, "output full list of unplaced tags")
  40         err = flags.Parse(args)
  41         if err == flag.ErrHelp {
  42                 err = nil
  43                 return 0
  44         } else if err != nil {
  45                 return 2
  46         }
  47
  48         if *pprof != "" {
  49                 go func() {
  50                         log.Println(http.ListenAndServe(*pprof, nil))
  51                 }()
  52         }
  53
  54         if !*runlocal {
  55                 if *outputFilename != "-" {
  56                         err = errors.New("cannot specify output file in container mode: not implemented")
  57                         return 1
  58                 }
  59                 runner := arvadosContainerRunner{
  60                         Name:        "lightning stats",
  61                         Client:      arvados.NewClientFromEnv(),
  62                         ProjectUUID: *projectUUID,
  63                         RAM:         16000000000,
  64                         VCPUs:       1,
  65                         Priority:    *priority,
  66                 }
  67                 err = runner.TranslatePaths(inputFilename)
  68                 if err != nil {
  69                         return 1
  70                 }
  71                 runner.Args = []string{"stats", "-local=true", fmt.Sprintf("-debug-unplaced=%v", cmd.debugUnplaced), "-i", *inputFilename, "-o", "/mnt/output/stats.json"}
  72                 var output string
  73                 output, err = runner.Run()
  74                 if err != nil {
  75                         return 1
  76                 }
  77                 fmt.Fprintln(stdout, output+"/stats.json")
  78                 return 0
  79         }
  80
  81         var input io.ReadCloser
  82         if *inputFilename == "-" {
  83                 input = ioutil.NopCloser(stdin)
  84         } else {
  85                 input, err = os.Open(*inputFilename)
  86                 if err != nil {
  87                         return 1
  88                 }
  89                 defer input.Close()
  90         }
  91
  92         var output io.WriteCloser
  93         if *outputFilename == "-" {
  94                 output = nopCloser{stdout}
  95         } else {
  96                 output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0777)
  97                 if err != nil {
  98                         return 1
  99                 }
 100                 defer output.Close()
 101         }
 102
 103         bufw := bufio.NewWriter(output)
 104         err = cmd.doStats(input, strings.HasSuffix(*inputFilename, ".gz"), bufw)
 105         if err != nil {
 106                 return 1
 107         }
 108         err = bufw.Flush()
 109         if err != nil {
 110                 return 1
 111         }
 112         err = output.Close()
 113         if err != nil {
 114                 return 1
 115         }
 116         return 0
 117 }
 118
 119 func (cmd *statscmd) doStats(input io.Reader, gz bool, output io.Writer) error {
 120         var ret struct {
 121                 Genomes          int
 122                 CalledBases      []int64
 123                 Tags             int
 124                 TagsPlacedNTimes []int // a[x]==y means there were y tags that placed x times
 125                 TileVariants     int
 126                 VariantsBySize   []int
 127                 NCVariantsBySize []int
 128                 UnplacedTags     []string `json:",omitempty"`
 129         }
 130
 131         var tagSet [][]byte
 132         var tagPlacements []int
 133         tileVariantCalls := map[tileLibRef]int{}
 134         err := DecodeLibrary(input, gz, func(ent *LibraryEntry) error {
 135                 ret.Genomes += len(ent.CompactGenomes)
 136                 ret.TileVariants += len(ent.TileVariants)
 137                 if len(ent.TagSet) > 0 {
 138                         if ret.Tags > 0 {
 139                                 return errors.New("invalid input: contains multiple tagsets")
 140                         }
 141                         ret.Tags = len(ent.TagSet)
 142                         tagSet = ent.TagSet
 143                 }
 144                 for _, tv := range ent.TileVariants {
 145                         if need := 1 + len(tv.Sequence) - len(ret.VariantsBySize); need > 0 {
 146                                 ret.VariantsBySize = append(ret.VariantsBySize, make([]int, need)...)
 147                                 ret.NCVariantsBySize = append(ret.NCVariantsBySize, make([]int, need)...)
 148                         }
 149
 150                         calls := 0
 151                         hasNoCalls := false
 152                         for _, b := range tv.Sequence {
 153                                 if b == 'a' || b == 'c' || b == 'g' || b == 't' {
 154                                         calls++
 155                                 } else {
 156                                         hasNoCalls = true
 157                                 }
 158                         }
 159
 160                         if hasNoCalls {
 161                                 ret.NCVariantsBySize[len(tv.Sequence)]++
 162                         } else {
 163                                 ret.VariantsBySize[len(tv.Sequence)]++
 164                         }
 165
 166                         tileVariantCalls[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = calls
 167                 }
 168                 for _, g := range ent.CompactGenomes {
 169                         if need := (len(g.Variants)+1)/2 - len(tagPlacements); need > 0 {
 170                                 tagPlacements = append(tagPlacements, make([]int, need)...)
 171                         }
 172                         calledBases := int64(0)
 173                         for idx, v := range g.Variants {
 174                                 if v > 0 {
 175                                         tagPlacements[idx/2]++
 176                                         calledBases += int64(tileVariantCalls[tileLibRef{Tag: tagID(idx / 2), Variant: v}])
 177                                 }
 178                         }
 179                         ret.CalledBases = append(ret.CalledBases, calledBases)
 180                 }
 181                 return nil
 182         })
 183         if err != nil {
 184                 return err
 185         }
 186         for id, p := range tagPlacements {
 187                 for len(ret.TagsPlacedNTimes) <= p {
 188                         ret.TagsPlacedNTimes = append(ret.TagsPlacedNTimes, 0)
 189                 }
 190                 ret.TagsPlacedNTimes[p]++
 191                 if cmd.debugUnplaced && p == 0 {
 192                         ret.UnplacedTags = append(ret.UnplacedTags, fmt.Sprintf("%d %s", id, tagSet[id]))
 193                 }
 194         }
 195
 196         return json.NewEncoder(output).Encode(ret)
 197 }