Option to skip/ignore out-of-order tags.

[lightning.git] / import.go

diff --git a/import.go b/import.go
index e6b86afd81ca22038c025c669e39a6fd3a0c3b88..9c933da3dec02c2cbf359d730acfe4872972b37c 100644 (file)
--- a/import.go
+++ b/import.go
@@ -31,6 +31,7 @@ type importer struct {
        outputFile     string
        projectUUID    string
        runLocal       bool
+       skipOOO        bool
        encoder        *gob.Encoder
 }
 
@@ -48,6 +49,7 @@ func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, std
        flags.StringVar(&cmd.outputFile, "o", "-", "output `file`")
        flags.StringVar(&cmd.projectUUID, "project", "", "project `UUID` for output data")
        flags.BoolVar(&cmd.runLocal, "local", false, "run on local host (default: run in an arvados container)")
+       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`")
        err = flags.Parse(args)
@@ -193,7 +195,7 @@ func (cmd *importer) loadTileLibrary() (*tileLibrary, error) {
                return nil, fmt.Errorf("cannot tile: tag library is empty")
        }
        log.Printf("tag library %s load done", cmd.tagLibraryFile)
-       return &tileLibrary{taglib: &taglib}, nil
+       return &tileLibrary{taglib: &taglib, skipOOO: cmd.skipOOO}, nil
 }
 
 func listInputFiles(paths []string) (files []string, err error) {
@@ -293,8 +295,11 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                        }
                        flat := make([]tileVariantID, ntags*2)
                        for i := 0; i < ntags; i++ {
-                               flat[i*2] = variants[0][i]
-                               flat[i*2+1] = variants[1][i]
+                               for hap := 0; hap < 2; hap++ {
+                                       if i < len(variants[hap]) {
+                                               flat[i*2+hap] = variants[hap][i]
+                                       }
+                               }
                        }
                        err := cmd.encoder.Encode(LibraryEntry{
                                CompactGenomes: []CompactGenome{{Name: infile, Variants: flat}},