Option to export one vcf/csv file per chromosome.

[lightning.git] / vcf2fasta.go

diff --git a/vcf2fasta.go b/vcf2fasta.go
index f3faccf4f2b4738e756e6545b2a99dd564878112..2f840ee73f0e9bcc62a9f360dbbb85ca616acfeb 100644 (file)
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -1,4 +1,4 @@
-package main
+package lightning
 
 import (
        "bufio"
@@ -285,7 +285,12 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
 
                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)