-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
import (
"bufio"
"sync"
"syscall"
- "git.arvados.org/arvados.git/sdk/go/arvados"
+ "github.com/klauspost/pgzip"
log "github.com/sirupsen/logrus"
)
mask bool
gvcfRegionsPy string
gvcfRegionsPyData []byte
+ gvcfType string
projectUUID string
outputDir string
runLocal bool
vcpus int
+ batchArgs
stderr io.Writer
}
flags.StringVar(&cmd.genomeFile, "genome", "", "reference genome `file`")
flags.BoolVar(&cmd.mask, "mask", false, "mask uncalled regions (default: output hom ref)")
flags.StringVar(&cmd.gvcfRegionsPy, "gvcf-regions.py", "https://raw.githubusercontent.com/lijiayong/gvcf_regions/master/gvcf_regions.py", "source of gvcf_regions.py")
+ flags.StringVar(&cmd.gvcfType, "gvcf-type", "gatk", "gvcf_type argument to gvcf_regions.py: gatk, complete_genomics, freebayes")
flags.StringVar(&cmd.projectUUID, "project", "", "project `UUID` for containers and output data")
flags.StringVar(&cmd.outputDir, "output-dir", "", "output directory")
flags.IntVar(&cmd.vcpus, "vcpus", 0, "number of VCPUs to request for arvados container (default: 2*number of input files, max 32)")
flags.BoolVar(&cmd.runLocal, "local", false, "run on local host (default: run in an arvados container)")
+ cmd.batchArgs.Flags(flags)
priority := flags.Int("priority", 500, "container request priority")
pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
err = flags.Parse(args)
if err != nil {
return 1
}
- if cmd.vcpus = len(infiles) * 2; cmd.vcpus > 32 {
+ batchsize := (len(infiles) + cmd.batchArgs.batches - 1) / cmd.batchArgs.batches
+ if cmd.vcpus = batchsize * 2; cmd.vcpus > 32 {
cmd.vcpus = 32
}
}
runner := arvadosContainerRunner{
Name: "lightning vcf2fasta",
- Client: arvados.NewClientFromEnv(),
+ Client: arvadosClientFromEnv,
ProjectUUID: cmd.projectUUID,
RAM: 2<<30 + int64(cmd.vcpus)<<28,
VCPUs: cmd.vcpus,
Priority: *priority,
+ KeepCache: 2,
+ APIAccess: true,
Mounts: map[string]map[string]interface{}{
"/gvcf_regions.py": map[string]interface{}{
"kind": "text",
},
},
}
- if cmd.mask {
- runner.RAM += int64(cmd.vcpus) << 31
- }
err = runner.TranslatePaths(&cmd.refFile, &cmd.genomeFile)
if err != nil {
return 1
return 1
}
}
- runner.Args = append([]string{"vcf2fasta",
- "-local=true",
- "-ref", cmd.refFile, fmt.Sprintf("-mask=%v", cmd.mask),
- "-genome", cmd.genomeFile,
- "-gvcf-regions.py", "/gvcf_regions.py",
- "-output-dir", "/mnt/output"}, inputs...)
- var output string
- output, err = runner.Run()
+ var outputs []string
+ outputs, err = cmd.batchArgs.RunBatches(context.Background(), func(ctx context.Context, batch int) (string, error) {
+ runner := runner
+ if cmd.mask {
+ runner.RAM += int64(cmd.vcpus) << 31
+ }
+ runner.Args = []string{"vcf2fasta",
+ "-local=true",
+ "-ref", cmd.refFile, fmt.Sprintf("-mask=%v", cmd.mask),
+ "-genome", cmd.genomeFile,
+ "-gvcf-regions.py", "/gvcf_regions.py",
+ "-gvcf-type", cmd.gvcfType,
+ "-output-dir", "/mnt/output",
+ }
+ runner.Args = append(runner.Args, cmd.batchArgs.Args(batch)...)
+ runner.Args = append(runner.Args, inputs...)
+ log.Printf("batch %d: %v", batch, runner.Args)
+ return runner.RunContext(ctx)
+ })
if err != nil {
return 1
}
- fmt.Fprintln(stdout, output)
+ fmt.Fprintln(stdout, strings.Join(outputs, " "))
return 0
}
if err != nil {
return 1
}
+ infiles = cmd.batchArgs.Slice(infiles)
type job struct {
vcffile string
return fmt.Errorf("error opening output file: %s", err)
}
defer outf.Close()
- gzipw := gzip.NewWriter(outf)
+ bufw := bufio.NewWriterSize(outf, 8*1024*1024)
+ gzipw := pgzip.NewWriter(bufw)
defer gzipw.Close()
var maskfifo string // filename of mask fifo if we're running bedtools, otherwise ""
if cmd.mask {
chrSize := map[string]int{}
- vcffile, err := os.Open(infile)
+ vcffile, err := open(infile)
if err != nil {
return err
}
defer vcffile.Close()
var rdr io.Reader = vcffile
+ rdr = bufio.NewReaderSize(rdr, 8*1024*1024)
if strings.HasSuffix(infile, ".gz") {
rdr, err = gzip.NewReader(vcffile)
if err != nil {
if err = scanner.Err(); err != nil {
return fmt.Errorf("error scanning input file %q: %s", infile, err)
}
+
var regions bytes.Buffer
- bedargs := []string{"python2", "-", "--gvcf_type", "gatk", infile}
+ bedargs := []string{"python2", "-"}
+ if cmd.gvcfType == "complete_genomics_pass_all" {
+ bedargs = append(bedargs,
+ "--ignore_phrases", "CNV", "INS:ME",
+ "--unreported_is_called",
+ )
+ } else if cmd.gvcfType != "" {
+ bedargs = append(bedargs, "--gvcf_type", cmd.gvcfType)
+ }
+ bedargs = append(bedargs, infile)
bed := exec.CommandContext(ctx, bedargs[0], bedargs[1:]...)
bed.Stdin = bytes.NewBuffer(cmd.gvcfRegionsPyData)
bed.Stdout = ®ions
// Read chromosome sizes from genome file in
// case any weren't specified in the VCF
// header.
- genomeFile, err := os.Open(cmd.genomeFile)
+ genomeFile, err := open(cmd.genomeFile)
if err != nil {
return fmt.Errorf("error opening genome file %q: %s", cmd.genomeFile, err)
}
errs <- fmt.Errorf("bcftools consensus: %s", err)
return
}
+ log.Printf("exited %v", consensus.Args)
err = gzipw.Close()
if err != nil {
errs <- err
return
}
+ err = bufw.Flush()
+ if err != nil {
+ errs <- err
+ return
+ }
errs <- outf.Close()
}()
if resp.StatusCode != http.StatusOK {
return fmt.Errorf("get %q: http status %d", cmd.gvcfRegionsPy, resp.StatusCode)
}
- buf, err := ioutil.ReadAll(resp.Body)
+ buf, err := io.ReadAll(resp.Body)
if err != nil {
return fmt.Errorf("get %q: read body: %s", cmd.gvcfRegionsPy, err)
}
projects / lightning.git / blobdiff