+++ /dev/null
-package main
-
-import (
- "bufio"
- "encoding/gob"
- "errors"
- "flag"
- "fmt"
- "io"
- "io/ioutil"
- "net/http"
- _ "net/http/pprof"
- "os"
-
- "git.arvados.org/arvados.git/sdk/go/arvados"
- log "github.com/sirupsen/logrus"
-)
-
-type filterer struct {
- output io.Writer
-}
-
-func (cmd *filterer) 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)
- pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
- runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
- projectUUID := flags.String("project", "", "project `UUID` for output data")
- inputFilename := flags.String("i", "-", "input `file`")
- outputFilename := flags.String("o", "-", "output `file`")
- maxvariants := flags.Int("max-variants", -1, "drop tiles with more than `N` variants")
- mincoverage := flags.Float64("min-coverage", 1, "drop tiles with coverage less than `P` across all haplotypes (0 < P ≤ 1)")
- maxtag := flags.Int("max-tag", -1, "drop tiles with tag ID > `N`")
- err = flags.Parse(args)
- if err == flag.ErrHelp {
- err = nil
- return 0
- } else if err != nil {
- return 2
- }
- cmd.output = stdout
-
- if *pprof != "" {
- go func() {
- log.Println(http.ListenAndServe(*pprof, nil))
- }()
- }
-
- if !*runlocal {
- if *outputFilename != "-" {
- err = errors.New("cannot specify output file in container mode: not implemented")
- return 1
- }
- runner := arvadosContainerRunner{
- Name: "lightning filter",
- Client: arvados.NewClientFromEnv(),
- ProjectUUID: *projectUUID,
- RAM: 64000000000,
- VCPUs: 2,
- }
- err = runner.TranslatePaths(inputFilename)
- if err != nil {
- return 1
- }
- runner.Args = []string{"filter", "-local=true",
- "-i", *inputFilename,
- "-o", "/mnt/output/library.gob",
- "-max-variants", fmt.Sprintf("%d", *maxvariants),
- "-min-coverage", fmt.Sprintf("%f", *mincoverage),
- "-max-tag", fmt.Sprintf("%d", *maxtag),
- }
- var output string
- output, err = runner.Run()
- if err != nil {
- return 1
- }
- fmt.Fprintln(stdout, output+"/library.gob")
- return 0
- }
-
- var infile io.ReadCloser
- if *inputFilename == "-" {
- infile = ioutil.NopCloser(stdin)
- } else {
- infile, err = os.Open(*inputFilename)
- if err != nil {
- return 1
- }
- defer infile.Close()
- }
- log.Print("reading")
- cgs, err := ReadCompactGenomes(infile)
- if err != nil {
- return 1
- }
- err = infile.Close()
- if err != nil {
- return 1
- }
- log.Printf("reading done, %d genomes", len(cgs))
-
- log.Print("filtering")
- ntags := 0
- for _, cg := range cgs {
- if ntags < len(cg.Variants)/2 {
- ntags = len(cg.Variants) / 2
- }
- if *maxvariants < 0 {
- continue
- }
- maxVariantID := tileVariantID(*maxvariants)
- for idx, variant := range cg.Variants {
- if variant > maxVariantID {
- for _, cg := range cgs {
- if len(cg.Variants) > idx {
- cg.Variants[idx & ^1] = 0
- cg.Variants[idx|1] = 0
- }
- }
- }
- }
- }
-
- if *maxtag >= 0 && ntags > *maxtag {
- ntags = *maxtag
- for i, cg := range cgs {
- if len(cg.Variants) > *maxtag*2 {
- cgs[i].Variants = cg.Variants[:*maxtag*2]
- }
- }
- }
-
- if *mincoverage < 1 {
- mincov := int(*mincoverage * float64(len(cgs)*2))
- cov := make([]int, ntags)
- for _, cg := range cgs {
- for idx, variant := range cg.Variants {
- if variant > 0 {
- cov[idx>>1]++
- }
- }
- }
- for tag, c := range cov {
- if c < mincov {
- for _, cg := range cgs {
- if len(cg.Variants) > tag*2 {
- cg.Variants[tag*2] = 0
- cg.Variants[tag*2+1] = 0
- }
- }
- }
- }
- }
-
- log.Print("filtering done")
-
- var outfile io.WriteCloser
- if *outputFilename == "-" {
- outfile = nopCloser{cmd.output}
- } else {
- outfile, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0777)
- if err != nil {
- return 1
- }
- defer outfile.Close()
- }
- w := bufio.NewWriter(outfile)
- enc := gob.NewEncoder(w)
- log.Print("writing")
- err = enc.Encode(LibraryEntry{
- CompactGenomes: cgs,
- })
- if err != nil {
- return 1
- }
- log.Print("writing done")
- err = w.Flush()
- if err != nil {
- return 1
- }
- err = outfile.Close()
- if err != nil {
- return 1
- }
- return 0
-}
projects / lightning.git / blobdiff