Write hgvs-based numpy matrix.

[lightning.git] / annotate.go

diff --git a/annotate.go b/annotate.go
index b792119b20f84fd281639642a00d4d053a935d77..b1f20df98b72d83f9bda88888fa20791a46b4ea0 100644 (file)
--- a/annotate.go
+++ b/annotate.go
@@ -23,10 +23,11 @@ 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 {
@@ -242,13 +243,10 @@ 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 +297,9 @@ 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)
+                                       }
                                }
                        }()
                }