-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
import (
"bufio"
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", cmd.gvcfType, 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
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)
}