Fix variant numbering.

[lightning.git] / slicenumpy.go

diff --git a/slicenumpy.go b/slicenumpy.go
index 5c55b35af0a26eabb9217be302a8401e22cb0042..4d3bd2745db43ba2c372c1385b339ece8ae131d3 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -280,10 +280,14 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                        defer throttleCPU.Release()
                                        count := make(map[[blake2b.Size256]byte]int, len(variants))
                                        for _, cg := range cgs {
-                                               idx := (tag - tagstart) * 2
-                                               if int(idx) < len(cg.Variants) {
-                                                       count[variants[cg.Variants[idx]].Blake2b]++
-                                                       count[variants[cg.Variants[idx+1]].Blake2b]++
+                                               idx := int(tag-tagstart) * 2
+                                               if idx < len(cg.Variants) {
+                                                       for allele := 0; allele < 2; allele++ {
+                                                               v := cg.Variants[idx+allele]
+                                                               if v > 0 && len(variants[v].Sequence) > 0 {
+                                                                       count[variants[v].Blake2b]++
+                                                               }
+                                                       }
                                                }
                                        }
                                        // hash[i] will be the hash of