19566: Test p-value vs. Python.

[lightning.git] / exportnumpy.go

diff --git a/exportnumpy.go b/exportnumpy.go
index 8815b4b26a705bd3877507244c6b091db83e74d4..698180b7545664ad53ce2e6002032b802fde4f5c 100644 (file)
--- a/exportnumpy.go
+++ b/exportnumpy.go
@@ -62,6 +62,9 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
                return 0
        } else if err != nil {
                return 2
+       } else if flags.NArg() > 0 {
+               err = fmt.Errorf("errant command line arguments after parsed flags: %v", flags.Args())
+               return 2
        }
 
        if *pprof != "" {
@@ -112,7 +115,7 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
                retainTileSequences: true,
                compactGenomes:      map[string][]tileVariantID{},
        }
-       err = tilelib.LoadDir(context.Background(), *inputDir, nil)
+       err = tilelib.LoadDir(context.Background(), *inputDir)
        if err != nil {
                return 1
        }
@@ -404,22 +407,20 @@ func cgs2array(tilelib *tileLibrary, names []string, lowqual []map[tileVariantID
        return
 }
 
-func chooseTiles(tilelib *tileLibrary, regionsFilename string, expandRegions int) (drop []bool, err error) {
-       if regionsFilename == "" {
-               return
-       }
+func makeMask(regionsFilename string, expandRegions int) (*mask, error) {
+       log.Printf("makeMask: reading %s", regionsFilename)
        rfile, err := zopen(regionsFilename)
        if err != nil {
-               return
+               return nil, err
        }
        defer rfile.Close()
-       regions, err := ioutil.ReadAll(rfile)
+       regions, err := io.ReadAll(rfile)
        if err != nil {
-               return
+               return nil, err
        }
 
-       log.Print("chooseTiles: building mask")
-       mask := &mask{}
+       log.Print("makeMask: building mask")
+       var mask mask
        for _, line := range bytes.Split(regions, []byte{'\n'}) {
                if bytes.HasPrefix(line, []byte{'#'}) {
                        continue
@@ -443,14 +444,24 @@ func chooseTiles(tilelib *tileLibrary, regionsFilename string, expandRegions int
                                // GFF/GTF
                                end++
                        } else {
-                               err = fmt.Errorf("cannot parse input line as BED or GFF/GTF: %q", line)
-                               return
+                               return nil, fmt.Errorf("cannot parse input line as BED or GFF/GTF: %q", line)
                        }
                }
                mask.Add(refseqname, start-expandRegions, end+expandRegions)
        }
-       log.Print("chooseTiles: mask.Freeze")
+       log.Print("makeMask: mask.Freeze")
        mask.Freeze()
+       return &mask, nil
+}
+
+func chooseTiles(tilelib *tileLibrary, regionsFilename string, expandRegions int) (drop []bool, err error) {
+       if regionsFilename == "" {
+               return
+       }
+       mask, err := makeMask(regionsFilename, expandRegions)
+       if err != nil {
+               return
+       }
 
        tagset := tilelib.taglib.Tags()
        if len(tagset) == 0 {
@@ -560,5 +571,6 @@ func trimFilenameForLabel(s string) string {
        s = strings.TrimSuffix(s, ".2")
        s = strings.TrimSuffix(s, ".gz")
        s = strings.TrimSuffix(s, ".vcf")
+       s = strings.Replace(s, ",", "-", -1)
        return s
 }