Write deletions as "TAA T" instead of "AA .".

refs #17763

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

diff --git a/anno2vcf.go b/anno2vcf.go
index 3be030036d7c20f817f95a43439a24aa6a5f8f4b..a1a320ff34e2e2f592e4f385769c8b46cc917821 100644 (file)
--- a/anno2vcf.go
+++ b/anno2vcf.go
@@ -143,15 +143,18 @@ func (cmd *anno2vcf) RunCommand(prog string, args []string, stdin io.Reader, std
                                }
                                del := fields[6]
                                ins := fields[7]
-                               if len(del) == 0 && len(fields) >= 9 {
+                               if (len(del) == 0 || len(ins) == 0) && len(fields) >= 9 {
                                        // "123,,AA,T" means 123insAA
                                        // preceded by T. We record it
-                                       // here as 122TdelinsTAA to
+                                       // here as "122 T TAA" to
                                        // avoid writing an empty
-                                       // "ref" field in our VCF.
-                                       del = append([]byte(nil), fields[8]...)
-                                       ins = append(append([]byte(nil), del...), ins...)
-                                       position -= int64(len(del))
+                                       // "ref" field in our
+                                       // VCF. Similarly, we record
+                                       // deletions as "122 TAA T"
+                                       // rather than "123 AA .".
+                                       del = append(append(make([]byte, 0, len(fields[8])+len(del)), fields[8]...), del...)
+                                       ins = append(append(make([]byte, 0, len(fields[8])+len(ins)), fields[8]...), ins...)
+                                       position -= int64(len(fields[8]))
                                } else {
                                        del = append([]byte(nil), del...)
                                        ins = append([]byte(nil), ins...)