-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
import (
"bufio"
var regions bytes.Buffer
bedargs := []string{"python2", "-"}
- if cmd.gvcfType != "" {
+ 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)