-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
import (
"bufio"
"compress/gzip"
+ "context"
"encoding/gob"
+ "encoding/json"
"errors"
"flag"
"fmt"
"io"
- "log"
+ "io/ioutil"
"net/http"
_ "net/http/pprof"
"os"
"sync/atomic"
"time"
- "git.arvados.org/arvados.git/sdk/go/arvados"
+ "github.com/klauspost/pgzip"
+ log "github.com/sirupsen/logrus"
)
type importer struct {
- tagLibraryFile string
- refFile string
- outputFile string
- projectUUID string
- runLocal bool
- encoder *gob.Encoder
+ tagLibraryFile string
+ refFile string
+ outputFile string
+ projectUUID string
+ loglevel string
+ priority int
+ runLocal bool
+ skipOOO bool
+ outputTiles bool
+ saveIncompleteTiles bool
+ outputStats string
+ matchChromosome *regexp.Regexp
+ encoder *gob.Encoder
+ retainAfterEncoding bool // keep imported genomes/refseqs in memory after writing to disk
+ batchArgs
}
func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
flags.SetOutput(stderr)
flags.StringVar(&cmd.tagLibraryFile, "tag-library", "", "tag library fasta `file`")
flags.StringVar(&cmd.refFile, "ref", "", "reference fasta `file`")
- flags.StringVar(&cmd.outputFile, "o", "", "output `file`")
+ flags.StringVar(&cmd.outputFile, "o", "-", "output `file`")
flags.StringVar(&cmd.projectUUID, "project", "", "project `UUID` for output data")
flags.BoolVar(&cmd.runLocal, "local", false, "run on local host (default: run in an arvados container)")
+ flags.BoolVar(&cmd.skipOOO, "skip-ooo", false, "skip out-of-order tags")
+ flags.BoolVar(&cmd.outputTiles, "output-tiles", false, "include tile variant sequences in output file")
+ flags.BoolVar(&cmd.saveIncompleteTiles, "save-incomplete-tiles", false, "treat tiles with no-calls as regular tiles")
+ flags.StringVar(&cmd.outputStats, "output-stats", "", "output stats to `file` (json)")
+ cmd.batchArgs.Flags(flags)
+ matchChromosome := flags.String("match-chromosome", "^(chr)?([0-9]+|X|Y|MT?)$", "import chromosomes that match the given `regexp`")
+ flags.IntVar(&cmd.priority, "priority", 500, "container request priority")
pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
+ flags.StringVar(&cmd.loglevel, "loglevel", "info", "logging threshold (trace, debug, info, warn, error, fatal, or panic)")
err = flags.Parse(args)
if err == flag.ErrHelp {
err = nil
}()
}
+ lvl, err := log.ParseLevel(cmd.loglevel)
+ if err != nil {
+ return 2
+ }
+ log.SetLevel(lvl)
+
+ cmd.matchChromosome, err = regexp.Compile(*matchChromosome)
+ if err != nil {
+ return 1
+ }
+
if !cmd.runLocal {
- runner := arvadosContainerRunner{
- Name: "lightning import",
- Client: arvados.NewClientFromEnv(),
- ProjectUUID: cmd.projectUUID,
- RAM: 30000000000,
- VCPUs: 16,
- }
- err = runner.TranslatePaths(&cmd.tagLibraryFile, &cmd.refFile, &cmd.outputFile)
- if err != nil {
- return 1
- }
- inputs := flags.Args()
- for i := range inputs {
- err = runner.TranslatePaths(&inputs[i])
- if err != nil {
- return 1
- }
- }
- if cmd.outputFile == "" {
- cmd.outputFile = "/mnt/output/library.gob"
- } else {
- // Not yet implemented, but this should write
- // the collection to an existing collection,
- // possibly even an in-place update.
- err = errors.New("cannot specify output file in container mode: not implemented")
- return 1
- }
- runner.Args = append([]string{"import", "-local=true", "-tag-library", cmd.tagLibraryFile, "-ref", cmd.refFile, "-o", cmd.outputFile}, inputs...)
- err = runner.Run()
+ err = cmd.runBatches(stdout, flags.Args())
if err != nil {
return 1
}
if err != nil {
return 1
}
+ infiles = cmd.batchArgs.Slice(infiles)
- tilelib, err := cmd.loadTileLibrary()
+ taglib, err := cmd.loadTagLibrary()
if err != nil {
return 1
}
- go func() {
- for range time.Tick(10 * time.Second) {
- log.Printf("tilelib.Len() == %d", tilelib.Len())
- }
- }()
- var output io.WriteCloser
- if cmd.outputFile == "" {
- output = nopCloser{stdout}
+ var outw, outf io.WriteCloser
+ if cmd.outputFile == "-" {
+ outw = nopCloser{stdout}
} else {
- output, err = os.OpenFile(cmd.outputFile, os.O_CREATE|os.O_WRONLY, 0777)
+ outf, err = os.OpenFile(cmd.outputFile, os.O_CREATE|os.O_WRONLY, 0777)
if err != nil {
return 1
}
- defer output.Close()
+ defer outf.Close()
+ if strings.HasSuffix(cmd.outputFile, ".gz") {
+ outw = pgzip.NewWriter(outf)
+ } else {
+ outw = outf
+ }
}
- bufw := bufio.NewWriter(output)
+ bufw := bufio.NewWriterSize(outw, 64*1024*1024)
cmd.encoder = gob.NewEncoder(bufw)
+ tilelib := &tileLibrary{taglib: taglib, retainNoCalls: cmd.saveIncompleteTiles, skipOOO: cmd.skipOOO}
+ if cmd.outputTiles {
+ cmd.encoder.Encode(LibraryEntry{TagSet: taglib.Tags()})
+ tilelib.encoder = cmd.encoder
+ }
+ go func() {
+ for range time.Tick(10 * time.Minute) {
+ log.Printf("tilelib.Len() == %d", tilelib.Len())
+ }
+ }()
+
err = cmd.tileInputs(tilelib, infiles)
if err != nil {
return 1
if err != nil {
return 1
}
- err = output.Close()
+ err = outw.Close()
if err != nil {
return 1
}
+ if outf != nil && outf != outw {
+ err = outf.Close()
+ if err != nil {
+ return 1
+ }
+ }
return 0
}
-func (cmd *importer) tileFasta(tilelib *tileLibrary, infile string) (tileSeq, error) {
+func (cmd *importer) runBatches(stdout io.Writer, inputs []string) error {
+ if cmd.outputFile != "-" {
+ // Not yet implemented, but this should write
+ // the collection to an existing collection,
+ // possibly even an in-place update.
+ return errors.New("cannot specify output file in container mode: not implemented")
+ }
+ runner := arvadosContainerRunner{
+ Name: "lightning import",
+ Client: arvadosClientFromEnv,
+ ProjectUUID: cmd.projectUUID,
+ APIAccess: true,
+ RAM: 350000000000,
+ VCPUs: 96,
+ Priority: cmd.priority,
+ KeepCache: 1,
+ }
+ err := runner.TranslatePaths(&cmd.tagLibraryFile, &cmd.refFile, &cmd.outputFile)
+ if err != nil {
+ return err
+ }
+ for i := range inputs {
+ err = runner.TranslatePaths(&inputs[i])
+ if err != nil {
+ return err
+ }
+ }
+
+ outputs, err := cmd.batchArgs.RunBatches(context.Background(), func(ctx context.Context, batch int) (string, error) {
+ runner := runner
+ if cmd.batches > 1 {
+ runner.Name += fmt.Sprintf(" (batch %d of %d)", batch, cmd.batches)
+ }
+ runner.Args = []string{"import",
+ "-local=true",
+ "-loglevel=" + cmd.loglevel,
+ "-pprof=:6061",
+ fmt.Sprintf("-skip-ooo=%v", cmd.skipOOO),
+ fmt.Sprintf("-output-tiles=%v", cmd.outputTiles),
+ fmt.Sprintf("-save-incomplete-tiles=%v", cmd.saveIncompleteTiles),
+ "-match-chromosome", cmd.matchChromosome.String(),
+ "-output-stats", "/mnt/output/stats.json",
+ "-tag-library", cmd.tagLibraryFile,
+ "-ref", cmd.refFile,
+ "-o", "/mnt/output/library.gob.gz",
+ }
+ runner.Args = append(runner.Args, cmd.batchArgs.Args(batch)...)
+ runner.Args = append(runner.Args, inputs...)
+ return runner.RunContext(ctx)
+ })
+ if err != nil {
+ return err
+ }
+ var outfiles []string
+ for _, o := range outputs {
+ outfiles = append(outfiles, o+"/library.gob.gz")
+ }
+ fmt.Fprintln(stdout, strings.Join(outfiles, " "))
+ return nil
+}
+
+func (cmd *importer) tileFasta(tilelib *tileLibrary, infile string, isRef bool) (tileSeq, []importStats, error) {
var input io.ReadCloser
- input, err := os.Open(infile)
+ input, err := open(infile)
if err != nil {
- return nil, err
+ return nil, nil, err
}
defer input.Close()
+ input = ioutil.NopCloser(bufio.NewReaderSize(input, 8*1024*1024))
if strings.HasSuffix(infile, ".gz") {
- input, err = gzip.NewReader(input)
+ input, err = pgzip.NewReader(input)
if err != nil {
- return nil, err
+ return nil, nil, err
}
defer input.Close()
}
- return tilelib.TileFasta(infile, input)
+ return tilelib.TileFasta(infile, input, cmd.matchChromosome, isRef)
}
-func (cmd *importer) loadTileLibrary() (*tileLibrary, error) {
+func (cmd *importer) loadTagLibrary() (*tagLibrary, error) {
log.Printf("tag library %s load starting", cmd.tagLibraryFile)
- f, err := os.Open(cmd.tagLibraryFile)
+ f, err := open(cmd.tagLibraryFile)
if err != nil {
return nil, err
}
defer f.Close()
- var rdr io.ReadCloser = f
+ rdr := ioutil.NopCloser(bufio.NewReaderSize(f, 64*1024*1024))
if strings.HasSuffix(cmd.tagLibraryFile, ".gz") {
- rdr, err = gzip.NewReader(f)
+ rdr, err = gzip.NewReader(rdr)
if err != nil {
return nil, fmt.Errorf("%s: gzip: %s", cmd.tagLibraryFile, err)
}
return nil, fmt.Errorf("cannot tile: tag library is empty")
}
log.Printf("tag library %s load done", cmd.tagLibraryFile)
- return &tileLibrary{taglib: &taglib}, nil
+ return &taglib, nil
}
+var (
+ vcfFilenameRe = regexp.MustCompile(`\.vcf(\.gz)?$`)
+ fasta1FilenameRe = regexp.MustCompile(`\.1\.fa(sta)?(\.fa(sta)?)?(\.gz)?$`)
+ fasta2FilenameRe = regexp.MustCompile(`\.2\.fa(sta)?(\.fa(sta)?)?(\.gz)?$`)
+ fastaFilenameRe = regexp.MustCompile(`\.fa(sta)?(\.gz)?$`)
+)
+
func listInputFiles(paths []string) (files []string, err error) {
for _, path := range paths {
if fi, err := os.Stat(path); err != nil {
return nil, fmt.Errorf("%s: stat failed: %s", path, err)
} else if !fi.IsDir() {
- if !strings.HasSuffix(path, ".2.fasta") || strings.HasSuffix(path, ".2.fasta.gz") {
+ if !fasta2FilenameRe.MatchString(path) {
files = append(files, path)
}
continue
}
sort.Strings(names)
for _, name := range names {
- if strings.HasSuffix(name, ".vcf") || strings.HasSuffix(name, ".vcf.gz") {
+ if vcfFilenameRe.MatchString(name) {
files = append(files, filepath.Join(path, name))
- } else if strings.HasSuffix(name, ".1.fasta") || strings.HasSuffix(name, ".1.fasta.gz") {
+ } else if fastaFilenameRe.MatchString(name) && !fasta2FilenameRe.MatchString(name) {
files = append(files, filepath.Join(path, name))
}
}
d.Close()
}
for _, file := range files {
- if strings.HasSuffix(file, ".1.fasta") || strings.HasSuffix(file, ".1.fasta.gz") {
- continue
- } else if _, err := os.Stat(file + ".csi"); err == nil {
- continue
- } else if _, err = os.Stat(file + ".tbi"); err == nil {
+ if fastaFilenameRe.MatchString(file) {
continue
+ } else if vcfFilenameRe.MatchString(file) {
+ if _, err := os.Stat(file + ".csi"); err == nil {
+ continue
+ } else if _, err = os.Stat(file + ".tbi"); err == nil {
+ continue
+ } else {
+ return nil, fmt.Errorf("%s: cannot read without .tbi or .csi index file", file)
+ }
} else {
- return nil, fmt.Errorf("%s: cannot read without .tbi or .csi index file", file)
+ return nil, fmt.Errorf("don't know how to handle filename %s", file)
}
}
return
starttime := time.Now()
errs := make(chan error, 1)
todo := make(chan func() error, len(infiles)*2)
+ allstats := make([][]importStats, len(infiles)*2)
var encodeJobs sync.WaitGroup
- for _, infile := range infiles {
- infile := infile
+ for idx, infile := range infiles {
+ idx, infile := idx, infile
var phases sync.WaitGroup
phases.Add(2)
variants := make([][]tileVariantID, 2)
- if strings.HasSuffix(infile, ".1.fasta") || strings.HasSuffix(infile, ".1.fasta.gz") {
+ if fasta1FilenameRe.MatchString(infile) {
todo <- func() error {
defer phases.Done()
- log.Printf("%s starting", infile)
+ log.Printf("%s (sample.1) starting tiling", infile)
defer log.Printf("%s done", infile)
- tseqs, err := cmd.tileFasta(tilelib, infile)
- variants[0] = tseqs.Variants()
+ tseqs, stats, err := cmd.tileFasta(tilelib, infile, false)
+ allstats[idx*2] = stats
+ var kept, dropped int
+ variants[0], kept, dropped = tseqs.Variants()
+ log.Printf("%s (sample.1) found %d unique tags plus %d repeats", infile, kept, dropped)
return err
}
- infile2 := regexp.MustCompile(`\.1\.fasta(\.gz)?$`).ReplaceAllString(infile, `.2.fasta$1`)
+ infile2 := fasta1FilenameRe.ReplaceAllString(infile, `.2.fa$1$2$4`)
todo <- func() error {
defer phases.Done()
- log.Printf("%s starting", infile2)
+ log.Printf("%s (sample.2) starting tiling", infile2)
defer log.Printf("%s done", infile2)
- tseqs, err := cmd.tileFasta(tilelib, infile2)
- variants[1] = tseqs.Variants()
+ tseqs, stats, err := cmd.tileFasta(tilelib, infile2, false)
+ allstats[idx*2+1] = stats
+ var kept, dropped int
+ variants[1], kept, dropped = tseqs.Variants()
+ log.Printf("%s (sample.2) found %d unique tags plus %d repeats", infile2, kept, dropped)
return err
}
- } else {
+ } else if fastaFilenameRe.MatchString(infile) {
+ todo <- func() error {
+ defer phases.Done()
+ defer phases.Done()
+ log.Printf("%s (reference) starting tiling", infile)
+ defer log.Printf("%s done", infile)
+ tseqs, stats, err := cmd.tileFasta(tilelib, infile, true)
+ allstats[idx*2] = stats
+ if err != nil {
+ return err
+ }
+ totlen := 0
+ for _, tseq := range tseqs {
+ totlen += len(tseq)
+ }
+ log.Printf("%s (reference) tiled %d seqs, total len %d", infile, len(tseqs), totlen)
+
+ if cmd.retainAfterEncoding {
+ tilelib.mtx.Lock()
+ if tilelib.refseqs == nil {
+ tilelib.refseqs = map[string]map[string][]tileLibRef{}
+ }
+ tilelib.refseqs[infile] = tseqs
+ tilelib.mtx.Unlock()
+ }
+
+ return cmd.encoder.Encode(LibraryEntry{
+ CompactSequences: []CompactSequence{{Name: infile, TileSequences: tseqs}},
+ })
+ }
+ // Don't write out a CompactGenomes entry
+ continue
+ } else if vcfFilenameRe.MatchString(infile) {
for phase := 0; phase < 2; phase++ {
phase := phase
todo <- func() error {
defer phases.Done()
log.Printf("%s phase %d starting", infile, phase+1)
defer log.Printf("%s phase %d done", infile, phase+1)
- tseqs, err := cmd.tileGVCF(tilelib, infile, phase)
- variants[phase] = tseqs.Variants()
+ tseqs, stats, err := cmd.tileGVCF(tilelib, infile, phase)
+ allstats[idx*2] = stats
+ var kept, dropped int
+ variants[phase], kept, dropped = tseqs.Variants()
+ log.Printf("%s phase %d found %d unique tags plus %d repeats", infile, phase+1, kept, dropped)
return err
}
}
+ } else {
+ panic(fmt.Sprintf("bug: unhandled filename %q", infile))
}
encodeJobs.Add(1)
go func() {
if len(errs) > 0 {
return
}
- ntags := len(variants[0])
- if ntags < len(variants[1]) {
- ntags = len(variants[1])
- }
- flat := make([]tileVariantID, ntags*2)
- for i := 0; i < ntags; i++ {
- flat[i*2] = variants[0][i]
- flat[i*2+1] = variants[1][i]
- }
+ variants := flatten(variants)
err := cmd.encoder.Encode(LibraryEntry{
- CompactGenomes: []CompactGenome{{Name: infile, Variants: flat}},
+ CompactGenomes: []CompactGenome{{Name: infile, Variants: variants}},
})
if err != nil {
select {
default:
}
}
+ if cmd.retainAfterEncoding {
+ tilelib.mtx.Lock()
+ if tilelib.compactGenomes == nil {
+ tilelib.compactGenomes = make(map[string][]tileVariantID)
+ }
+ tilelib.compactGenomes[infile] = variants
+ tilelib.mtx.Unlock()
+ }
}()
}
go close(todo)
var tileJobs sync.WaitGroup
- running := int64(runtime.NumCPU())
- for i := 0; i < runtime.NumCPU(); i++ {
+ var running int64
+ for i := 0; i < runtime.GOMAXPROCS(-1); i++ {
tileJobs.Add(1)
+ atomic.AddInt64(&running, 1)
go func() {
defer tileJobs.Done()
defer atomic.AddInt64(&running, -1)
}
}
remain := len(todo) + int(atomic.LoadInt64(&running)) - 1
- ttl := time.Now().Sub(starttime) * time.Duration(remain) / time.Duration(cap(todo)-remain)
- eta := time.Now().Add(ttl)
- log.Printf("progress %d/%d, eta %v (%v)", cap(todo)-remain, cap(todo), eta, ttl)
+ if remain < cap(todo) {
+ ttl := time.Now().Sub(starttime) * time.Duration(remain) / time.Duration(cap(todo)-remain)
+ eta := time.Now().Add(ttl)
+ log.Printf("progress %d/%d, eta %v (%v)", cap(todo)-remain, cap(todo), eta, ttl)
+ }
}
}()
}
tileJobs.Wait()
+ if len(errs) > 0 {
+ // Must not wait on encodeJobs in this case. If the
+ // tileJobs goroutines exited early, some funcs in
+ // todo haven't been called, so the corresponding
+ // encodeJobs will wait forever.
+ return <-errs
+ }
encodeJobs.Wait()
+
go close(errs)
- return <-errs
+ err := <-errs
+ if err != nil {
+ return err
+ }
+
+ if cmd.outputStats != "" {
+ f, err := os.OpenFile(cmd.outputStats, os.O_CREATE|os.O_WRONLY, 0666)
+ if err != nil {
+ return err
+ }
+ var flatstats []importStats
+ for _, stats := range allstats {
+ flatstats = append(flatstats, stats...)
+ }
+ err = json.NewEncoder(f).Encode(flatstats)
+ if err != nil {
+ return err
+ }
+ }
+
+ return nil
}
-func (cmd *importer) tileGVCF(tilelib *tileLibrary, infile string, phase int) (tileseq tileSeq, err error) {
+func (cmd *importer) tileGVCF(tilelib *tileLibrary, infile string, phase int) (tileseq tileSeq, stats []importStats, err error) {
if cmd.refFile == "" {
err = errors.New("cannot import vcf: reference data (-ref) not specified")
return
return
}
defer consensus.Wait()
- tileseq, err = tilelib.TileFasta(fmt.Sprintf("%s phase %d", infile, phase+1), stdout)
+ tileseq, stats, err = tilelib.TileFasta(fmt.Sprintf("%s phase %d", infile, phase+1), stdout, cmd.matchChromosome, false)
if err != nil {
return
}
}
return
}
+
+func flatten(variants [][]tileVariantID) []tileVariantID {
+ ntags := 0
+ for _, v := range variants {
+ if ntags < len(v) {
+ ntags = len(v)
+ }
+ }
+ flat := make([]tileVariantID, ntags*2)
+ for i := 0; i < ntags; i++ {
+ for hap := 0; hap < 2; hap++ {
+ if i < len(variants[hap]) {
+ flat[i*2+hap] = variants[hap][i]
+ }
+ }
+ }
+ return flat
+}
projects / lightning.git / blobdiff