X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/53f36ff0323547f835b1b068324429f53ce7220c..66cf9d08ca8504cdb660ed44738622b90f7fd42f:/annotate.go

diff --git a/annotate.go b/annotate.go
index b792119b20..25651889aa 100644
--- a/annotate.go
+++ b/annotate.go
@@ -1,3 +1,7 @@
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
 package lightning
 
 import (
@@ -23,10 +27,11 @@ import (
 )
 
 type annotatecmd struct {
-	dropTiles   []bool
-	variantHash bool
-	maxTileSize int
-	tag2tagid   map[string]tagID
+	dropTiles        []bool
+	variantHash      bool
+	maxTileSize      int
+	tag2tagid        map[string]tagID
+	reportAnnotation func(tag tagID, outcol int, variant tileVariantID, refname string, seqname string, pdi hgvs.Variant)
 }
 
 func (cmd *annotatecmd) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
@@ -113,7 +118,7 @@ func (cmd *annotatecmd) RunCommand(prog string, args []string, stdin io.Reader,
 		retainNoCalls:       true,
 		retainTileSequences: true,
 	}
-	err = tilelib.LoadGob(context.Background(), input, strings.HasSuffix(*inputFilename, ".gz"), nil)
+	err = tilelib.LoadGob(context.Background(), input, strings.HasSuffix(*inputFilename, ".gz"))
 	if err != nil {
 		return 1
 	}
@@ -242,13 +247,10 @@ func (cmd *annotatecmd) annotateSequence(throttle *throttle, outch chan<- string
 		outcol := outcol
 		refstart, ok := tilestart[tag]
 		if !ok {
-			// Tag didn't place on this
-			// reference sequence. (It
-			// might place on the same
-			// chromosome in a genome
-			// anyway, but we don't output
-			// the annotations that would
-			// result.)
+			// Tag didn't place on this reference
+			// sequence. (It might place on the same
+			// chromosome in a genome anyway, but we don't
+			// output the annotations that would result.)
 			// outch <- fmt.Sprintf("%d,%d,-1%s\n", tag, outcol, refnamefield)
 			continue
 		}
@@ -299,6 +301,9 @@ func (cmd *annotatecmd) annotateSequence(throttle *throttle, outch chan<- string
 						varid = fmt.Sprintf("%d", variant)
 					}
 					outch <- fmt.Sprintf("%d,%d,%s%s,%s:g.%s\n", tag, outcol, varid, refnamefield, seqname, diff.String())
+					if cmd.reportAnnotation != nil {
+						cmd.reportAnnotation(tag, outcol, variant, refname, seqname, diff)
+					}
 				}
 			}()
 		}