From: Tom Clegg <tom@tomclegg.ca>
Date: Thu, 4 Nov 2021 18:11:42 +0000 (-0400)
Subject: Write deletions as "TAA T" instead of "AA .".
X-Git-Url: https://git.arvados.org/lightning.git/commitdiff_plain/a44451aca10112b46db186b55bfdeac2c525cced

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 3be030036d..a1a320ff34 100644
--- 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...)