Avoid empty "ref" field in anno2vcf output.

refs #17763

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

diff --git a/anno2vcf.go b/anno2vcf.go
index 47af7e5caf55ea81d566a6dd7a15e4b979b2899b..3be030036d7c20f817f95a43439a24aa6a5f8f4b 100644 (file)
--- a/anno2vcf.go
+++ b/anno2vcf.go
@@ -131,8 +131,8 @@ func (cmd *anno2vcf) RunCommand(prog string, args []string, stdin io.Reader, std
                                        return nil
                                }
                                fields := bytes.Split(line, []byte{','})
-                               if len(fields) != 8 {
-                                       return fmt.Errorf("%s line %d: wrong number of fields (%d != %d): %q", fi.Name(), lineIdx+1, len(fields), 8, line)
+                               if len(fields) < 8 {
+                                       return fmt.Errorf("%s line %d: wrong number of fields (%d < %d): %q", fi.Name(), lineIdx+1, len(fields), 8, line)
                                }
                                tile, _ := strconv.ParseInt(string(fields[0]), 10, 64)
                                variant, _ := strconv.ParseInt(string(fields[2]), 10, 64)
@@ -141,12 +141,27 @@ func (cmd *anno2vcf) RunCommand(prog string, args []string, stdin io.Reader, std
                                if calls[seq] == nil {
                                        calls[seq] = make([]*call, 0, len(lines)/50)
                                }
+                               del := fields[6]
+                               ins := fields[7]
+                               if len(del) == 0 && len(fields) >= 9 {
+                                       // "123,,AA,T" means 123insAA
+                                       // preceded by T. We record it
+                                       // here as 122TdelinsTAA 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))
+                               } else {
+                                       del = append([]byte(nil), del...)
+                                       ins = append([]byte(nil), ins...)
+                               }
                                calls[seq] = append(calls[seq], &call{
                                        tile:      int(tile),
                                        variant:   int(variant),
                                        position:  int(position),
-                                       deletion:  append([]byte(nil), fields[6]...),
-                                       insertion: append([]byte(nil), fields[7]...),
+                                       deletion:  del,
+                                       insertion: ins,
                                })
                        }
                        mtx.Lock()

diff --git a/slicenumpy.go b/slicenumpy.go
index 5aa97ac5a7c44707b03720ac6631eaa03599ce54..fff70d7379f81aa90e50c2d917bbf5c268ffee7a 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -349,7 +349,7 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                        diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
                                        for _, diff := range diffs {
                                                diff.Position += rt.pos
-                                               fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s\n", tag, outcol, remap[v], rt.seqname, diff.String(), rt.seqname, diff.Position, diff.Ref, diff.New)
+                                               fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s,%s\n", tag, outcol, remap[v], rt.seqname, diff.String(), rt.seqname, diff.Position, diff.Ref, diff.New, diff.Left)
                                        }
                                }
                        }