anno2vcf.go

   1 // Copyright (C) The Lightning Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package lightning
   6
   7 import (
   8         "bufio"
   9         "bytes"
  10         "flag"
  11         "fmt"
  12         "io"
  13         "io/ioutil"
  14         "net/http"
  15         _ "net/http/pprof"
  16         "os"
  17         "runtime"
  18         "sort"
  19         "strconv"
  20         "strings"
  21         "sync"
  22
  23         "git.arvados.org/arvados.git/sdk/go/arvados"
  24         log "github.com/sirupsen/logrus"
  25 )
  26
  27 type anno2vcf struct {
  28 }
  29
  30 func (cmd *anno2vcf) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  31         var err error
  32         defer func() {
  33                 if err != nil {
  34                         fmt.Fprintf(stderr, "%s\n", err)
  35                 }
  36         }()
  37         flags := flag.NewFlagSet("", flag.ContinueOnError)
  38         flags.SetOutput(stderr)
  39         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  40         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  41         projectUUID := flags.String("project", "", "project `UUID` for output data")
  42         priority := flags.Int("priority", 500, "container request priority")
  43         inputDir := flags.String("input-dir", "./in", "input `directory`")
  44         outputDir := flags.String("output-dir", "./out", "output `directory`")
  45         err = flags.Parse(args)
  46         if err == flag.ErrHelp {
  47                 err = nil
  48                 return 0
  49         } else if err != nil {
  50                 return 2
  51         }
  52
  53         if *pprof != "" {
  54                 go func() {
  55                         log.Println(http.ListenAndServe(*pprof, nil))
  56                 }()
  57         }
  58
  59         if !*runlocal {
  60                 runner := arvadosContainerRunner{
  61                         Name:        "lightning anno2vcf",
  62                         Client:      arvados.NewClientFromEnv(),
  63                         ProjectUUID: *projectUUID,
  64                         RAM:         500000000000,
  65                         VCPUs:       64,
  66                         Priority:    *priority,
  67                         KeepCache:   2,
  68                         APIAccess:   true,
  69                 }
  70                 err = runner.TranslatePaths(inputDir)
  71                 if err != nil {
  72                         return 1
  73                 }
  74                 runner.Args = []string{"anno2vcf", "-local=true",
  75                         "-pprof", ":6060",
  76                         "-input-dir", *inputDir,
  77                         "-output-dir", "/mnt/output",
  78                 }
  79                 var output string
  80                 output, err = runner.Run()
  81                 if err != nil {
  82                         return 1
  83                 }
  84                 fmt.Fprintln(stdout, output)
  85                 return 0
  86         }
  87
  88         d, err := open(*inputDir)
  89         if err != nil {
  90                 log.Print(err)
  91                 return 1
  92         }
  93         defer d.Close()
  94         fis, err := d.Readdir(-1)
  95         if err != nil {
  96                 log.Print(err)
  97                 return 1
  98         }
  99         d.Close()
 100         sort.Slice(fis, func(i, j int) bool { return fis[i].Name() < fis[j].Name() })
 101
 102         type call struct {
 103                 tile      int
 104                 variant   int
 105                 position  int
 106                 deletion  []byte
 107                 insertion []byte
 108                 hgvsID    []byte
 109         }
 110         allcalls := map[string][]*call{}
 111         var mtx sync.Mutex
 112         thr := throttle{Max: runtime.GOMAXPROCS(0)}
 113         log.Print("reading input files")
 114         for _, fi := range fis {
 115                 if !strings.HasSuffix(fi.Name(), "annotations.csv") {
 116                         continue
 117                 }
 118                 filename := *inputDir + "/" + fi.Name()
 119                 thr.Go(func() error {
 120                         log.Printf("reading %s", filename)
 121                         buf, err := ioutil.ReadFile(filename)
 122                         if err != nil {
 123                                 return fmt.Errorf("%s: %s", filename, err)
 124                         }
 125                         lines := bytes.Split(buf, []byte{'\n'})
 126                         calls := map[string][]*call{}
 127                         for lineIdx, line := range lines {
 128                                 if len(line) == 0 {
 129                                         continue
 130                                 }
 131                                 if lineIdx&0xff == 0 && thr.Err() != nil {
 132                                         return nil
 133                                 }
 134                                 fields := bytes.Split(line, []byte{','})
 135                                 if len(fields) < 8 {
 136                                         return fmt.Errorf("%s line %d: wrong number of fields (%d < %d): %q", fi.Name(), lineIdx+1, len(fields), 8, line)
 137                                 }
 138                                 hgvsID := fields[3]
 139                                 if len(hgvsID) < 2 {
 140                                         // "=" reference or ""
 141                                         // non-diffable tile variant
 142                                         continue
 143                                 }
 144                                 tile, _ := strconv.ParseInt(string(fields[0]), 10, 64)
 145                                 variant, _ := strconv.ParseInt(string(fields[2]), 10, 64)
 146                                 position, _ := strconv.ParseInt(string(fields[5]), 10, 64)
 147                                 seq := string(fields[4])
 148                                 if calls[seq] == nil {
 149                                         calls[seq] = make([]*call, 0, len(lines)/50)
 150                                 }
 151                                 del := fields[6]
 152                                 ins := fields[7]
 153                                 if (len(del) == 0 || len(ins) == 0) && len(fields) >= 9 {
 154                                         // "123,,AA,T" means 123insAA
 155                                         // preceded by T. We record it
 156                                         // here as "122 T TAA" to
 157                                         // avoid writing an empty
 158                                         // "ref" field in our
 159                                         // VCF. Similarly, we record
 160                                         // deletions as "122 TAA T"
 161                                         // rather than "123 AA .".
 162                                         del = append(append(make([]byte, 0, len(fields[8])+len(del)), fields[8]...), del...)
 163                                         ins = append(append(make([]byte, 0, len(fields[8])+len(ins)), fields[8]...), ins...)
 164                                         position -= int64(len(fields[8]))
 165                                 } else {
 166                                         del = append([]byte(nil), del...)
 167                                         ins = append([]byte(nil), ins...)
 168                                 }
 169                                 calls[seq] = append(calls[seq], &call{
 170                                         tile:      int(tile),
 171                                         variant:   int(variant),
 172                                         position:  int(position),
 173                                         deletion:  del,
 174                                         insertion: ins,
 175                                         hgvsID:    hgvsID,
 176                                 })
 177                         }
 178                         mtx.Lock()
 179                         for seq, seqcalls := range calls {
 180                                 allcalls[seq] = append(allcalls[seq], seqcalls...)
 181                         }
 182                         mtx.Unlock()
 183                         return nil
 184                 })
 185         }
 186         err = thr.Wait()
 187         if err != nil {
 188                 return 1
 189         }
 190         thr = throttle{Max: len(allcalls)}
 191         for seq, seqcalls := range allcalls {
 192                 seq, seqcalls := seq, seqcalls
 193                 thr.Go(func() error {
 194                         log.Printf("%s: sorting", seq)
 195                         sort.Slice(seqcalls, func(i, j int) bool {
 196                                 ii, jj := seqcalls[i], seqcalls[j]
 197                                 if cmp := ii.position - jj.position; cmp != 0 {
 198                                         return cmp < 0
 199                                 }
 200                                 if cmp := len(ii.deletion) - len(jj.deletion); cmp != 0 {
 201                                         return cmp < 0
 202                                 }
 203                                 if cmp := bytes.Compare(ii.insertion, jj.insertion); cmp != 0 {
 204                                         return cmp < 0
 205                                 }
 206                                 if cmp := ii.tile - jj.tile; cmp != 0 {
 207                                         return cmp < 0
 208                                 }
 209                                 return ii.variant < jj.variant
 210                         })
 211
 212                         vcfFilename := fmt.Sprintf("%s/annotations.%s.vcf", *outputDir, seq)
 213                         log.Printf("%s: writing %s", seq, vcfFilename)
 214
 215                         f, err := os.Create(vcfFilename)
 216                         if err != nil {
 217                                 return err
 218                         }
 219                         defer f.Close()
 220                         bufw := bufio.NewWriterSize(f, 1<<20)
 221                         _, err = fmt.Fprintf(bufw, `##fileformat=VCFv4.0
 222 ##INFO=<ID=TV,Number=.,Type=String,Description="tile-variant">
 223 #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
 224 `)
 225                         if err != nil {
 226                                 return err
 227                         }
 228                         placeholder := []byte{'.'}
 229                         for i := 0; i < len(seqcalls); {
 230                                 call := seqcalls[i]
 231                                 i++
 232                                 info := fmt.Sprintf("TV=,%d-%d,", call.tile, call.variant)
 233                                 for i < len(seqcalls) &&
 234                                         call.position == seqcalls[i].position &&
 235                                         len(call.deletion) == len(seqcalls[i].deletion) &&
 236                                         bytes.Equal(call.insertion, seqcalls[i].insertion) {
 237                                         call = seqcalls[i]
 238                                         i++
 239                                         info += fmt.Sprintf("%d-%d,", call.tile, call.variant)
 240                                 }
 241                                 deletion := call.deletion
 242                                 if len(deletion) == 0 {
 243                                         deletion = placeholder
 244                                 }
 245                                 insertion := call.insertion
 246                                 if len(insertion) == 0 {
 247                                         insertion = placeholder
 248                                 }
 249                                 _, err = fmt.Fprintf(bufw, "%s\t%d\t%s\t%s\t%s\t.\t.\t%s\n", seq, call.position, call.hgvsID, deletion, insertion, info)
 250                                 if err != nil {
 251                                         return err
 252                                 }
 253                         }
 254                         err = bufw.Flush()
 255                         if err != nil {
 256                                 return err
 257                         }
 258                         err = f.Close()
 259                         if err != nil {
 260                                 return err
 261                         }
 262                         log.Printf("%s: done", seq)
 263                         return nil
 264                 })
 265         }
 266         err = thr.Wait()
 267         if err != nil {
 268                 return 1
 269         }
 270         return 0
 271 }