Update git path.

[lightning.git] / import.go

diff --git a/import.go b/import.go
index d50843d079fcc608ff882d2b15607d067ab61793..a396636fcb324628a42b60b07d294d9cbba650ec 100644 (file)
--- a/import.go
+++ b/import.go
@@ -52,6 +52,7 @@ func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, std
        flags.BoolVar(&cmd.skipOOO, "skip-ooo", false, "skip out-of-order tags")
        priority := flags.Int("priority", 500, "container request priority")
        pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
+       loglevel := flags.String("loglevel", "info", "logging threshold (trace, debug, info, warn, error, fatal, or panic)")
        err = flags.Parse(args)
        if err == flag.ErrHelp {
                err = nil
@@ -72,6 +73,12 @@ func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, std
                }()
        }
 
+       lvl, err := log.ParseLevel(*loglevel)
+       if err != nil {
+               return 2
+       }
+       log.SetLevel(lvl)
+
        if !cmd.runLocal {
                runner := arvadosContainerRunner{
                        Name:        "lightning import",
@@ -101,7 +108,7 @@ func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, std
                        err = errors.New("cannot specify output file in container mode: not implemented")
                        return 1
                }
-               runner.Args = append([]string{"import", "-local=true", fmt.Sprintf("-skip-ooo=%v", cmd.skipOOO), "-tag-library", cmd.tagLibraryFile, "-ref", cmd.refFile, "-o", cmd.outputFile}, inputs...)
+               runner.Args = append([]string{"import", "-local=true", "-loglevel=" + *loglevel, fmt.Sprintf("-skip-ooo=%v", cmd.skipOOO), "-tag-library", cmd.tagLibraryFile, "-ref", cmd.refFile, "-o", cmd.outputFile}, inputs...)
                var output string
                output, err = runner.Run()
                if err != nil {
@@ -257,7 +264,9 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                                log.Printf("%s starting", infile)
                                defer log.Printf("%s done", infile)
                                tseqs, err := cmd.tileFasta(tilelib, infile)
-                               variants[0] = tseqs.Variants()
+                               var kept, dropped int
+                               variants[0], kept, dropped = tseqs.Variants()
+                               log.Printf("%s found %d unique tags plus %d repeats", infile, kept, dropped)
                                return err
                        }
                        infile2 := regexp.MustCompile(`\.1\.fasta(\.gz)?$`).ReplaceAllString(infile, `.2.fasta$1`)
@@ -266,7 +275,9 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                                log.Printf("%s starting", infile2)
                                defer log.Printf("%s done", infile2)
                                tseqs, err := cmd.tileFasta(tilelib, infile2)
-                               variants[1] = tseqs.Variants()
+                               var kept, dropped int
+                               variants[1], kept, dropped = tseqs.Variants()
+                               log.Printf("%s found %d unique tags plus %d repeats", infile, kept, dropped)
                                return err
                        }
                } else {
@@ -277,7 +288,9 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                                        log.Printf("%s phase %d starting", infile, phase+1)
                                        defer log.Printf("%s phase %d done", infile, phase+1)
                                        tseqs, err := cmd.tileGVCF(tilelib, infile, phase)
-                                       variants[phase] = tseqs.Variants()
+                                       var kept, dropped int
+                                       variants[phase], kept, dropped = tseqs.Variants()
+                                       log.Printf("%s phase %d found %d unique tags plus %d repeats", infile, phase+1, kept, dropped)
                                        return err
                                }
                        }