19566: Record number of p-value calculations performed.

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

diff --git a/slicenumpy.go b/slicenumpy.go
index 84d501b5c687114309be59a4e1211980265a11a3..0095cc4fa71a670cdda7287caeff14b018cd262e 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -8,6 +8,7 @@ import (
        "bufio"
        "bytes"
        "encoding/gob"
+       "encoding/json"
        "errors"
        "flag"
        "fmt"
@@ -53,6 +54,7 @@ type sliceNumpy struct {
        trainingSet     []int // samples index => training set index, or -1 if not in training set
        trainingSetSize int
        pvalue          func(onehot []bool) float64
+       pvalueCallCount int64
 }
 
 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
@@ -1195,6 +1197,17 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
                        if err != nil {
                                return err
                        }
+                       fnm = fmt.Sprintf("%s/stats.json", *outputDir)
+                       j, err := json.Marshal(map[string]interface{}{
+                               "pvalueCallCount": cmd.pvalueCallCount,
+                       })
+                       if err != nil {
+                               return err
+                       }
+                       err = os.WriteFile(fnm, j, 0777)
+                       if err != nil {
+                               return err
+                       }
                }
                if *onlyPCA {
                        cols := 0
@@ -1623,6 +1636,7 @@ func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantI
                if col < 4 && !cmd.includeVariant1 {
                        continue
                }
+               atomic.AddInt64(&cmd.pvalueCallCount, 1)
                p := cmd.pvalue(obs[col])
                if cmd.chi2PValue < 1 && !(p < cmd.chi2PValue) {
                        continue