package main
import (
+ "bufio"
"bytes"
"compress/gzip"
+ "context"
"errors"
"flag"
"fmt"
"os"
"os/exec"
"path/filepath"
+ "regexp"
"runtime"
+ "strconv"
"strings"
"sync"
"syscall"
},
},
}
- err = runner.TranslatePaths(&cmd.refFile)
+ 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), "-gvcf-regions.py", "/gvcf_regions.py", "-output-dir", "/mnt/output"}, inputs...)
+ 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()
if err != nil {
}
func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
+ ctx, cancel := context.WithCancel(context.Background())
+ defer cancel()
+
_, basename := filepath.Split(infile)
outfile := filepath.Join(cmd.outputDir, fmt.Sprintf("%s.%d.fasta.gz", basename, phase))
outf, err := os.OpenFile(outfile, os.O_CREATE|os.O_WRONLY, 0777)
var wg sync.WaitGroup
errs := make(chan error, 2)
if cmd.mask {
- if cmd.genomeFile == "" {
- return errors.New("cannot apply mask without -genome argument")
+ chrSize := map[string]int{}
+
+ vcffile, err := os.Open(infile)
+ if err != nil {
+ return err
+ }
+ defer vcffile.Close()
+ var rdr io.Reader = vcffile
+ if strings.HasSuffix(infile, ".gz") {
+ rdr, err = gzip.NewReader(vcffile)
+ if err != nil {
+ return err
+ }
+ }
+ contigre := regexp.MustCompile(`([^=,]*)=([^>,]*)`)
+ scanner := bufio.NewScanner(rdr)
+ for scanner.Scan() {
+ if s := scanner.Text(); !strings.HasPrefix(s, "##") {
+ break
+ } else if !strings.HasPrefix(s, "##contig=<") {
+ continue
+ } else {
+ kv := map[string]string{}
+ for _, m := range contigre.FindAllStringSubmatch(s[10:], -1) {
+ kv[m[1]] = m[2]
+ }
+ if kv["ID"] != "" && kv["length"] != "" {
+ chrSize[kv["ID"]], _ = strconv.Atoi(kv["length"])
+ }
+ }
+ }
+ if err = scanner.Err(); err != nil {
+ return fmt.Errorf("error scanning input file %q: %s", infile, err)
}
var regions bytes.Buffer
- bedargs := []string{"python", "-", "--gvcf_type", "gatk", infile}
- bed := exec.Command(bedargs[0], bedargs[1:]...)
+ bedargs := []string{"python2", "-", "--gvcf_type", "gatk", infile}
+ bed := exec.CommandContext(ctx, bedargs[0], bedargs[1:]...)
bed.Stdin = bytes.NewBuffer(cmd.gvcfRegionsPyData)
bed.Stdout = ®ions
bed.Stderr = cmd.stderr
log.Printf("running %v", bed.Args)
- err := bed.Run()
+ err = bed.Run()
log.Printf("exited %v", bed.Args)
if err != nil {
return fmt.Errorf("gvcf_regions: %s", err)
}
+ if cmd.genomeFile != "" {
+ // Read chromosome sizes from genome file in
+ // case any weren't specified in the VCF
+ // header.
+ genomeFile, err := os.Open(cmd.genomeFile)
+ if err != nil {
+ return fmt.Errorf("error opening genome file %q: %s", cmd.genomeFile, err)
+ }
+ scanner := bufio.NewScanner(genomeFile)
+ for scanner.Scan() {
+ var chr string
+ var size int
+ _, err := fmt.Sscanf(scanner.Text(), "%s\t%d", &chr, &size)
+ if err != nil {
+ return fmt.Errorf("error parsing genome file %q: %s", cmd.genomeFile, err)
+ }
+ if chrSize[chr] == 0 {
+ chrSize[chr] = size
+ }
+ }
+ if err = scanner.Err(); err != nil {
+ return fmt.Errorf("error scanning genome file %q: %s", cmd.genomeFile, err)
+ }
+ }
+
+ // "bedtools complement" expects the chromosome sizes
+ // ("genome file") to appear in the same order as the
+ // chromosomes in the input vcf, so we need to sort
+ // them.
+ scanner = bufio.NewScanner(bytes.NewBuffer(append([]byte(nil), regions.Bytes()...)))
+ var sortedGenomeFile bytes.Buffer
+ for scanner.Scan() {
+ var chr string
+ var size int
+ _, err := fmt.Sscanf(scanner.Text(), "%s\t%d", &chr, &size)
+ if err != nil {
+ return fmt.Errorf("error parsing gvcf_regions output: %s", err)
+ }
+ if size, ok := chrSize[chr]; ok {
+ fmt.Fprintf(&sortedGenomeFile, "%s\t%d\n", chr, size)
+ delete(chrSize, chr)
+ }
+ }
+
// The bcftools --mask argument needs to end in ".bed"
// in order to be parsed as a BED file, so we need to
// use a named pipe instead of stdin.
if err != nil {
return fmt.Errorf("mkfifo: %s", err)
}
+
+ // bedtools complement can't seem to read from a pipe
+ // reliably -- "Error: line number 1 of file
+ // /dev/stdin has 1 fields, but 3 were expected." --
+ // so we stage to a temp file.
+ regionsFile := filepath.Join(tempdir, "gvcf_regions.bed")
+ err = ioutil.WriteFile(regionsFile, regions.Bytes(), 0644)
+ if err != nil {
+ return err
+ }
+
wg.Add(1)
go func() {
defer wg.Done()
}
defer maskfifow.Close()
- bedcompargs := []string{"bedtools", "complement", "-i", "/dev/stdin", "-g", cmd.genomeFile}
+ bedcompargs := []string{"bedtools", "complement", "-i", regionsFile, "-g", "/dev/stdin"}
bedcompargs = maybeInDocker(bedcompargs, []string{cmd.genomeFile})
- bedcomp := exec.Command(bedcompargs[0], bedcompargs[1:]...)
- bedcomp.Stdin = ®ions
+ bedcomp := exec.CommandContext(ctx, bedcompargs[0], bedcompargs[1:]...)
+ bedcomp.Stdin = &sortedGenomeFile
bedcomp.Stdout = maskfifow
bedcomp.Stderr = cmd.stderr
log.Printf("running %v", bedcomp.Args)
}
consargs = maybeInDocker(consargs, mounts)
- consensus := exec.Command(consargs[0], consargs[1:]...)
+ consensus := exec.CommandContext(ctx, consargs[0], consargs[1:]...)
consensus.Stderr = os.Stderr
consensus.Stdout = gzipw
consensus.Stderr = cmd.stderr
for err := range errs {
if err != nil {
+ cancel()
wg.Wait()
return err
}
projects / lightning.git / blobdiff