19527: Output samples.csv earlier.

refs #19527

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

diff --git a/slicenumpy.go b/slicenumpy.go
index c53a8a13e32af163b08d93b03dcf20532d9d3485..6d8a531cbc866add507fefcb047cb2db7f72221b 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -286,6 +286,41 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
                cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
        }
 
+       {
+               samplesOutFilename := *outputDir + "/samples.csv"
+               log.Infof("writing sample metadata to %s", samplesOutFilename)
+               var f *os.File
+               f, err = os.Create(samplesOutFilename)
+               if err != nil {
+                       return err
+               }
+               defer f.Close()
+               for i, si := range cmd.samples {
+                       var cc, tv string
+                       if si.isCase {
+                               cc = "1"
+                       } else if si.isControl {
+                               cc = "0"
+                       }
+                       if si.isTraining {
+                               tv = "1"
+                       } else {
+                               tv = "0"
+                       }
+                       _, err = fmt.Fprintf(f, "%d,%s,%s,%s\n", i, si.id, cc, tv)
+                       if err != nil {
+                               err = fmt.Errorf("write %s: %w", samplesOutFilename, err)
+                               return err
+                       }
+               }
+               err = f.Close()
+               if err != nil {
+                       err = fmt.Errorf("close %s: %w", samplesOutFilename, err)
+                       return err
+               }
+               log.Print("done")
+       }
+
        log.Info("indexing reference tiles")
        type reftileinfo struct {
                variant  tileVariantID
@@ -1133,39 +1168,6 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
                        if err != nil {
                                return err
                        }
-
-                       samplesOutFilename := *outputDir + "/samples.csv"
-                       log.Infof("writing sample metadata to %s", samplesOutFilename)
-                       var f *os.File
-                       f, err = os.Create(samplesOutFilename)
-                       if err != nil {
-                               return err
-                       }
-                       defer f.Close()
-                       for i, si := range cmd.samples {
-                               var cc, tv string
-                               if si.isCase {
-                                       cc = "1"
-                               } else if si.isControl {
-                                       cc = "0"
-                               }
-                               if si.isTraining {
-                                       tv = "1"
-                               } else {
-                                       tv = "0"
-                               }
-                               _, err = fmt.Fprintf(f, "%d,%s,%s,%s\n", i, si.id, cc, tv)
-                               if err != nil {
-                                       err = fmt.Errorf("write %s: %w", samplesOutFilename, err)
-                                       return err
-                               }
-                       }
-                       err = f.Close()
-                       if err != nil {
-                               err = fmt.Errorf("close %s: %w", samplesOutFilename, err)
-                               return err
-                       }
-                       log.Print("done")
                }
                if *onlyPCA {
                        cols := 0