Mention undiffable variants in annotations, write -2 in hgvs matrix.

refs #18438

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

diff --git a/slicenumpy.go b/slicenumpy.go
index c5e48f09832f5a350b99330561c9d63549203f46..a8fdeb064eefa682437b0558958785b003ed81fc 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -376,8 +376,8 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                }
                                variants, ok := seq[tag]
                                if !ok {
                                }
                                variants, ok := seq[tag]
                                if !ok {

-                                       outcol++
-                                       continue
+                                       // how could we even have a reftile if there is no sequence data??
+                                       return fmt.Errorf("bug: have no variants for tag %d but reftile is %+v", tag, rt)

                                }
                                reftilestr := strings.ToUpper(string(rt.tiledata))
                                remap := variantRemap[tag-tagstart]
                                }
                                reftilestr := strings.ToUpper(string(rt.tiledata))
                                remap := variantRemap[tag-tagstart]


@@ -390,9 +390,11 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                                done[v] = true
                                        }
                                        if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
                                                done[v] = true
                                        }
                                        if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {

+                                               fmt.Fprintf(annow, "%d,%d,%d,.,%s,%d,.,,\n", tag, outcol, v, rt.seqname, rt.pos)

                                                continue
                                        }
                                        if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
                                                continue
                                        }
                                        if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {

+                                               fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)

                                                continue
                                        }
                                        diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
                                                continue
                                        }
                                        diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)


@@ -514,8 +516,14 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                }
                                for ph := 0; ph < 2; ph++ {
                                        for row := 0; row < rows; row++ {
                                }
                                for ph := 0; ph < 2; ph++ {
                                        for row := 0; row < rows; row++ {

-                                               if v := chunk[row*chunkcols+incol*2+ph]; int(v) == tileVariant {
-                                                       hgvscols[ph][row] = 1
+                                               v := chunk[row*chunkcols+incol*2+ph]
+                                               if int(v) == tileVariant {
+                                                       if len(hgvsID) == 0 {
+                                                               // we have the tile variant sequence, but the diff against ref didn't work out (see lendiff above)
+                                                               hgvscols[ph][row] = -2
+                                                       } else {
+                                                               hgvscols[ph][row] = 1
+                                                       }

                                                } else if v < 0 {
                                                        hgvscols[ph][row] = -1
                                                }
                                                } else if v < 0 {
                                                        hgvscols[ph][row] = -1
                                                }