19527: Fix one-hot matrix.

refs #19527

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

diff --git a/slicenumpy.go b/slicenumpy.go
index e787693da573e3275193f5add2c3bbb1fb397dfd..8eaec62bb219fc07c6106a7968350f18bd67aa3c 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -1547,22 +1547,30 @@ func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantI
        if coverage < cmd.minCoverage {
                return nil, nil
        }
+       // "observed" array for p-value calculation (training set
+       // only)
        obs := make([][]bool, (maxv+1)*2) // 2 slices (hom + het) for each variant#
+       // one-hot output (all samples)
+       outcols := make([][]int8, (maxv+1)*2)
        for i := range obs {
                obs[i] = make([]bool, cmd.trainingSetSize)
+               outcols[i] = make([]int8, len(cmd.cgnames))
        }
        for cgid, name := range cmd.cgnames {
                tsid := cmd.trainingSet[cgid]
-               if tsid < 0 {
-                       continue
-               }
                cgvars := cgs[name].Variants[tagoffset*2:]
                tv0, tv1 := remap[cgvars[0]], remap[cgvars[1]]
                for v := tileVariantID(1); v <= maxv; v++ {
                        if tv0 == v && tv1 == v {
-                               obs[v*2][tsid] = true
+                               if tsid >= 0 {
+                                       obs[v*2][tsid] = true
+                               }
+                               outcols[v*2][cgid] = 1
                        } else if tv0 == v || tv1 == v {
-                               obs[v*2+1][tsid] = true
+                               if tsid >= 0 {
+                                       obs[v*2+1][tsid] = true
+                               }
+                               outcols[v*2+1][cgid] = 1
                        }
                }
        }
@@ -1579,7 +1587,7 @@ func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantI
                if cmd.chi2PValue < 1 && !(p < cmd.chi2PValue) {
                        continue
                }
-               onehot = append(onehot, bool2int8(obs[col]))
+               onehot = append(onehot, outcols[col])
                xref = append(xref, onehotXref{
                        tag:     tag,
                        variant: tileVariantID(col >> 1),
@@ -1590,16 +1598,6 @@ func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantI
        return onehot, xref
 }
 
-func bool2int8(in []bool) []int8 {
-       out := make([]int8, len(in))
-       for i, v := range in {
-               if v {
-                       out[i] = 1
-               }
-       }
-       return out
-}
-
 // convert a []onehotXref with length N to a numpy-style []int32
 // matrix with N columns, one row per field of onehotXref struct.
 //