Pass gvcf-type to gvcf_regions.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

diff --git a/vcf2fasta.go b/vcf2fasta.go
index 2f02e44a28b8b9188ba8700c4ce15c88a08647c5..4044cfdeee5412ba1099d258359fea9eee792f86 100644 (file)
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -32,6 +32,7 @@ type vcf2fasta struct {
        mask              bool
        gvcfRegionsPy     string
        gvcfRegionsPyData []byte
+       gvcfType          string
        projectUUID       string
        outputDir         string
        runLocal          bool
@@ -53,6 +54,7 @@ func (cmd *vcf2fasta) RunCommand(prog string, args []string, stdin io.Reader, st
        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)")
@@ -135,6 +137,7 @@ func (cmd *vcf2fasta) RunCommand(prog string, args []string, stdin io.Reader, st
                        "-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"}, inputs...)
                var output string
                output, err = runner.Run()
@@ -265,7 +268,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
                        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", "-", "--gvcf_type", cmd.gvcfType, infile}
                bed := exec.CommandContext(ctx, bedargs[0], bedargs[1:]...)
                bed.Stdin = bytes.NewBuffer(cmd.gvcfRegionsPyData)
                bed.Stdout = &regions