--- /dev/null
+package main
+
+import (
+ "fmt"
+ "io"
+ "io/ioutil"
+ "os"
+ "os/exec"
+
+ "git.arvados.org/arvados.git/lib/cmd"
+)
+
+var (
+ handler = cmd.Multi(map[string]cmd.Handler{
+ "version": cmd.Version,
+ "-version": cmd.Version,
+ "--version": cmd.Version,
+
+ "gvcf2numpy": &gvcf2numpy{},
+ "build-docker-image": &buildDockerImage{},
+ })
+)
+
+func main() {
+ os.Exit(handler.RunCommand(os.Args[0], os.Args[1:], os.Stdin, os.Stdout, os.Stderr))
+}
+
+type buildDockerImage struct{}
+
+func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
+ tmpdir, err := ioutil.TempDir("", "")
+ if err != nil {
+ fmt.Fprint(stderr, err)
+ return 1
+ }
+ defer os.RemoveAll(tmpdir)
+ err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:10
+RUN apt-get update
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends bcftools samtools
+`), 0644)
+ if err != nil {
+ fmt.Fprint(stderr, err)
+ return 1
+ }
+ docker := exec.Command("docker", "build", "--tag=lightning-runtime", tmpdir)
+ docker.Stdout = os.Stdout
+ docker.Stderr = os.Stderr
+ err = docker.Run()
+ if err != nil {
+ return 1
+ }
+ return 0
+}
--- /dev/null
+module github.com/curii/lightning
+
+go 1.13
+
+require (
+ git.arvados.org/arvados.git v0.0.0-20200107160329-7db3857d78a0
+ gopkg.in/check.v1 v1.0.0-20161208181325-20d25e280405
+)
--- /dev/null
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+gopkg.in/yaml.v2 v2.2.4/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
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+rsc.io/getopt v0.0.0-20170811000552-20be20937449/go.mod h1:dhCdeqAxkyt5u3/sKRkUXuHaMXUu1Pt13GTQAM2xnig=
--- /dev/null
+package main
+
+import (
+ "compress/gzip"
+ "flag"
+ "fmt"
+ "io"
+ "log"
+ "os"
+ "os/exec"
+ "strings"
+ "sync"
+)
+
+type gvcf2numpy struct {
+ tagLibraryFile string
+ refFile string
+}
+
+func (cmd *gvcf2numpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
+ var err error
+ defer func() {
+ if err != nil {
+ fmt.Fprintf(stderr, "%s\n", err)
+ }
+ }()
+ flags := flag.NewFlagSet("", flag.ContinueOnError)
+ flags.SetOutput(stderr)
+ flags.StringVar(&cmd.tagLibraryFile, "tag-library", "", "tag library fasta `file`")
+ flags.StringVar(&cmd.refFile, "ref", "", "reference fasta `file`")
+ err = flags.Parse(args)
+ if err == flag.ErrHelp {
+ err = nil
+ return 0
+ } else if err != nil {
+ return 2
+ } else if cmd.refFile == "" || cmd.tagLibraryFile == "" {
+ fmt.Fprintln(os.Stderr, "cannot run without -tag-library and -ref arguments")
+ return 2
+ } else if flags.NArg() == 0 {
+ flags.Usage()
+ return 2
+ }
+ f, err := os.Open(cmd.tagLibraryFile)
+ if err != nil {
+ return 1
+ }
+ var rdr io.ReadCloser = f
+ if strings.HasSuffix(cmd.tagLibraryFile, ".gz") {
+ rdr, err = gzip.NewReader(f)
+ if err != nil {
+ err = fmt.Errorf("%s: gzip: %s", cmd.tagLibraryFile, err)
+ return 1
+ }
+ }
+ var taglib tagLibrary
+ err = taglib.Load(rdr)
+ if err != nil {
+ return 1
+ }
+ if taglib.Len() < 1 {
+ err = fmt.Errorf("cannot tile: tag library is empty")
+ return 1
+ }
+ tilelib := tileLibrary{taglib: &taglib}
+ err = cmd.tileGVCFs(&tilelib, flags.Args())
+ if err != nil {
+ return 1
+ }
+ return 0
+}
+
+func (cmd *gvcf2numpy) tileGVCFs(tilelib *tileLibrary, infiles []string) error {
+ errs := make(chan error)
+ var wg sync.WaitGroup
+ for _, infile := range infiles {
+ for phase := 0; phase < 2; phase++ {
+ wg.Add(1)
+ go func(infile string, phase int) {
+ defer wg.Done()
+ tseq, err := cmd.tileGVCF(tilelib, infile, phase)
+ if err != nil {
+ select {
+ case errs <- err:
+ default:
+ }
+ return
+ }
+ for chr, path := range tseq {
+ cmd.printVariants(fmt.Sprintf("%s chr %s phase %d", infile, chr, phase+1), path)
+ }
+ }(infile, phase)
+ }
+ }
+ go func() {
+ wg.Wait()
+ close(errs)
+ }()
+ if err := <-errs; err != nil {
+ return err
+ }
+ return nil
+}
+
+func (cmd *gvcf2numpy) printVariants(label string, path []tileLibRef) {
+ maxtag := tagID(-1)
+ for _, tvar := range path {
+ if maxtag < tvar.tag {
+ maxtag = tvar.tag
+ }
+ }
+ variant := make([]tileVariantID, maxtag+1)
+ for _, tvar := range path {
+ variant[tvar.tag] = tvar.variant
+ }
+
+ excerpt := variant
+ if len(excerpt) > 100 {
+ excerpt = excerpt[:100]
+ }
+ log.Printf("%s: %v...", label, excerpt)
+}
+
+func (cmd *gvcf2numpy) tileGVCF(tilelib *tileLibrary, infile string, phase int) (tileseq tileSeq, err error) {
+ args := []string{"bcftools", "consensus", "--fasta-ref", cmd.refFile, "-H", fmt.Sprint(phase + 1), infile}
+ if out, err := exec.Command("docker", "image", "ls", "-q", "lightning-runtime").Output(); err == nil && len(out) > 0 {
+ args = append([]string{
+ "docker", "run", "--rm",
+ "--volume=" + infile + ":" + infile + ":ro",
+ "--volume=" + infile + ".csi:" + infile + ".csi:ro",
+ "--volume=" + cmd.refFile + ":" + cmd.refFile + ":ro",
+ "lightning-runtime",
+ }, args...)
+ }
+ consensus := exec.Command(args[0], args[1:]...)
+ consensus.Stderr = os.Stderr
+ stdout, err := consensus.StdoutPipe()
+ if err != nil {
+ return
+ }
+ err = consensus.Start()
+ if err != nil {
+ return
+ }
+ tileseq, err = tilelib.TileFasta(stdout)
+ if err != nil {
+ return
+ }
+ err = stdout.Close()
+ if err != nil {
+ return
+ }
+ err = consensus.Wait()
+ if err != nil {
+ err = fmt.Errorf("%s phase %d: bcftools: %s", infile, phase, err)
+ return
+ }
+ return
+}
--- /dev/null
+package main
+
+import (
+ "bufio"
+ "bytes"
+ "fmt"
+ "io"
+)
+
+const tagmapKeySize = 24
+
+type tagmapKey [tagmapKeySize]byte
+
+type tagID int32
+
+type tagInfo struct {
+ id tagID // 0-based position in input tagset
+ tagseq []byte
+}
+
+type tagLibrary struct {
+ tagmap map[tagmapKey]tagInfo
+ keylen int
+}
+
+func (taglib *tagLibrary) Load(rdr io.Reader) error {
+ var seqs [][]byte
+ scanner := bufio.NewScanner(rdr)
+ for scanner.Scan() {
+ data := scanner.Bytes()
+ if len(data) > 0 && data[0] == '>' {
+ } else {
+ seqs = append(seqs, append([]byte(nil), data...))
+ }
+ }
+ if err := scanner.Err(); err != nil {
+ return err
+ }
+ return taglib.setTags(seqs)
+}
+
+type tagMatch struct {
+ id tagID
+ pos int
+}
+
+func (taglib *tagLibrary) FindAll(buf []byte, fn func(id tagID, pos int)) {
+ var key tagmapKey
+ for i := 0; i <= len(buf)-taglib.keylen; i++ {
+ copy(key[:taglib.keylen], buf[i:])
+ if taginfo, ok := taglib.tagmap[key]; !ok {
+ continue
+ } else if len(taginfo.tagseq) > taglib.keylen && (len(buf) < i+len(taginfo.tagseq) || !bytes.Equal(taginfo.tagseq, buf[i:i+len(taginfo.tagseq)])) {
+ // key portion matches, but not the entire tag
+ continue
+ } else {
+ fn(taginfo.id, i)
+ }
+ }
+}
+
+func (taglib *tagLibrary) Len() int {
+ return len(taglib.tagmap)
+}
+
+func (taglib *tagLibrary) setTags(tags [][]byte) error {
+ taglib.keylen = tagmapKeySize
+ for _, t := range tags {
+ if l := len(t); taglib.keylen > l {
+ taglib.keylen = l
+ }
+ }
+ taglib.tagmap = map[tagmapKey]tagInfo{}
+ for i, t := range tags {
+ t = bytes.ToLower(t)
+ var key tagmapKey
+ copy(key[:], t[:taglib.keylen])
+ if _, ok := taglib.tagmap[key]; ok {
+ return fmt.Errorf("first %d bytes of tag %d (%s) are not unique", taglib.keylen, i, key)
+ }
+ taglib.tagmap[key] = tagInfo{tagID(i), t}
+ }
+ return nil
+}
--- /dev/null
+package main
+
+import (
+ "bufio"
+ "fmt"
+ "io"
+ "math/rand"
+ "os"
+ "strings"
+ "testing"
+ "time"
+
+ "gopkg.in/check.v1"
+)
+
+func Test(t *testing.T) { check.TestingT(t) }
+
+type taglibSuite struct{}
+
+var _ = check.Suite(&taglibSuite{})
+
+func (s *taglibSuite) TestFindAllTinyData(c *check.C) {
+ pr, pw, err := os.Pipe()
+ c.Assert(err, check.IsNil)
+ go func() {
+ defer pw.Close()
+ fmt.Fprintf(pw, `>0000.00
+ggagaactgtgctccgccttcaga
+acacatgctagcgcgtcggggtgg
+gactctagcagagtggccagccac
+`)
+ }()
+ var taglib tagLibrary
+ err = taglib.Load(pr)
+ c.Assert(err, check.IsNil)
+ haystack := []byte(`ggagaactgtgctccgccttcagaccccccccccccccccccccacacatgctagcgcgtcggggtgggggggggggggggggggggggggggactctagcagagtggccagccac`)
+ var matches []tagMatch
+ taglib.FindAll(haystack, func(id tagID, pos int) {
+ matches = append(matches, tagMatch{id, pos})
+ })
+ c.Check(matches, check.DeepEquals, []tagMatch{{0, 0}, {1, 44}, {2, 92}})
+}
+
+func (s *taglibSuite) TestFindAllRealisticSize(c *check.C) {
+ start := time.Now()
+ acgt := []byte{'a', 'c', 'g', 't'}
+ haystack := make([]byte, 25000000) // ~1/2 smallest human chromosome
+ c.Logf("@%v haystack", time.Since(start))
+ rand.Read(haystack)
+ for i := range haystack {
+ haystack[i] = acgt[int(haystack[i]&3)]
+ }
+
+ tagcount := 12500
+ tagsize := 24
+ var tags []string
+ pr, pw := io.Pipe()
+ go func() {
+ defer pw.Close()
+ w := bufio.NewWriter(pw)
+ defer w.Flush()
+ used := map[string]bool{}
+ fmt.Fprint(w, ">000\n")
+ for i := 0; len(tags) < tagcount; i += (len(haystack) - tagsize) / tagcount {
+ i := i
+ tag := haystack[i : i+tagsize]
+ for used[string(tag)] {
+ i++
+ tag = haystack[i : i+tagsize]
+ }
+ used[string(tag)] = true
+ tags = append(tags, strings.ToLower(string(tag)))
+ w.Write(tag)
+ w.Write([]byte{'\n'})
+ }
+ }()
+ c.Logf("@%v build library", time.Since(start))
+ var taglib tagLibrary
+ err := taglib.Load(pr)
+ c.Assert(err, check.IsNil)
+ c.Logf("@%v find tags in input", time.Since(start))
+ var matches []tagMatch
+ taglib.FindAll(haystack, func(id tagID, pos int) {
+ matches = append(matches, tagMatch{id, pos})
+ })
+ c.Logf("@%v done", time.Since(start))
+ c.Check(matches[0], check.Equals, tagMatch{0, 0})
+ c.Check(matches[1].id, check.Equals, tagID(1))
+}
--- /dev/null
+package main
+
+import (
+ "bufio"
+ "bytes"
+ "crypto/md5"
+ "io"
+ "sync"
+)
+
+type tileVariantID int32 // 1-based
+
+type tileLibRef struct {
+ tag tagID
+ variant tileVariantID
+}
+
+type tileSeq map[string][]tileLibRef
+
+type tileLibrary struct {
+ taglib *tagLibrary
+ variant [][][md5.Size]byte
+ // count [][]int
+ seq map[[md5.Size]byte][]byte
+
+ mtx sync.Mutex
+}
+
+func (tilelib *tileLibrary) TileFasta(rdr io.Reader) (tileSeq, error) {
+ ret := tileSeq{}
+ flush := func(label string, fasta []byte) {
+ var path []tileLibRef
+ if len(fasta) == 0 {
+ return
+ }
+ tilestart := -1 // position in fasta of tile that ends here
+ tiletagid := tagID(-1) // tag id starting tile that ends here
+ tilelib.taglib.FindAll(fasta, func(id tagID, pos int) {
+ if tilestart >= 0 {
+ path = append(path, tilelib.getRef(tiletagid, fasta[tilestart:pos]))
+ // log.Printf("%q: tile %d is variant %d of tile %d", label, len(path), path[len(path)-1], id)
+ }
+ tilestart = pos
+ tiletagid = id
+ })
+ if tiletagid >= 0 {
+ path = append(path, tilelib.getRef(tiletagid, fasta[tilestart:]))
+ // log.Printf("%q: tile %d is variant %d of tile %d", label, len(path), path[len(path)-1], tiletagid)
+ }
+ ret[label] = path
+ }
+ var fasta []byte
+ var label string
+ scanner := bufio.NewScanner(rdr)
+ for scanner.Scan() {
+ buf := scanner.Bytes()
+ if len(buf) == 0 || buf[0] == '>' {
+ flush(label, fasta)
+ fasta = nil
+ label = string(buf[1:])
+ } else {
+ fasta = append(fasta, bytes.ToLower(buf)...)
+ }
+ }
+ if err := scanner.Err(); err != nil {
+ return nil, err
+ }
+ flush(label, fasta)
+ return ret, nil
+}
+
+// Return a tileLibRef for a tile with the given tag and sequence,
+// adding the sequence to the library if needed.
+func (tilelib *tileLibrary) getRef(tag tagID, seq []byte) tileLibRef {
+ tilelib.mtx.Lock()
+ defer tilelib.mtx.Unlock()
+ if tilelib.seq == nil {
+ tilelib.seq = map[[md5.Size]byte][]byte{}
+ }
+ for len(tilelib.variant) <= int(tag) {
+ tilelib.variant = append(tilelib.variant, nil)
+ }
+ seqhash := md5.Sum(seq)
+ for i, varhash := range tilelib.variant[tag] {
+ if varhash == seqhash {
+ return tileLibRef{tag: tag, variant: tileVariantID(i + 1)}
+ }
+ }
+ tilelib.variant[tag] = append(tilelib.variant[tag], seqhash)
+ tilelib.seq[seqhash] = append([]byte(nil), seq...)
+ return tileLibRef{tag: tag, variant: tileVariantID(len(tilelib.variant[tag]))}
+}
--- /dev/null
+package main
+
+type Tiler struct {
+}
+
+func newTiler(taglib *tagLibrary) *Tiler {
+ return &Tiler{}
+}
projects / lightning.git / commitdiff