BAM import issues

Dave OConnor

• September 22, 2025 00:47

Hi there,

I'm trying to get a BAM file to successfully import from a location on disk. I've indexed the BAM file. The combination of the BAM file and its reference sequences are fine if I import into the UI via drag-and-drop. However, when I try to import via my plug-in, I'm prompted to select a reference sequence. If I select the folder containing the reference sequences that I've imported via my plug-in, the BAM file is parsed correctly. 

Below is a snippet of how I'm trying to import the BAM file. Can you advise or provide a minimal example of how to import a BAM file and its reference sequence(s) via public APIs?

Thanks,

Dave

```

for (File bamFile : bamFiles) {

System.out.println(" Importing BAM file: " + bamFile.getName());

try {

// Import BAM directly to the database folder containing references

// This SHOULD ensure Geneious can find references automatically

WritableDatabaseServicetargetFolder;

if (!importedReferences.isEmpty() && folders.containsKey("References")) {

// Import to References folder where the reference sequences are

targetFolder = folders.get("References");

System.out.println(" Importing BAM directly to References folder with " +

importedReferences.size() + " reference(s)");

// Import BAM file directly to the folder

List<AnnotatedPluginDocument> docs = PluginUtilities.importDocumentsToDatabase(

bamFile, targetFolder, progressListener);

if (docs != null && !docs.isEmpty()) {

allImported.addAll(docs);

System.out.println(" Successfully imported BAM with " + docs.size() +

" alignment(s) to References folder");

for (AnnotatedPluginDocumentdoc: docs) {

System.out.println(" - " + doc.getName());

}

}

}

} catch (Exception e) {

logger.log(Level.WARNING, "Failed to import BAM file: " + bamFile.getName(), e);

}

}

```

0

• 

  Matthew Cheung

  • September 25, 2025 09:10

  Hi there,

  Our SAM/BAM importer needs to have both the BAM file and reference passed to its DocumentFileImporter.importDocumentsFromMultipleFilesReturningUnimported() method.

  Unfortunately this doesn't get used by any of our convenience utility classes, so you'll need to use it directly.  Here is an example of how you can do it.

  // Get importer
  DocumentFileImporter importer = PluginUtilities.getDocumentFileImporters().stream()
      .filter(imp ->
          Arrays.stream(imp.getPermissibleExtensions()).anyMatch(extension -> extension.equalsIgnoreCase(".bam"))
      ).findFirst()
      .orElseThrow(() -> new DocumentOperationException("No BAM importer available"));
  
  // Create a ImportCallback that stores the results in an ArrayList
  List<AnnotatedPluginDocument> imported = new ArrayList<>();
  DocumentFileImporter.ImportCallback callback = new DocumentFileImporter.ImportCallback() {
      @Override
      public AnnotatedPluginDocument addDocument(PluginDocument document) {
          AnnotatedPluginDocument apd = DocumentUtilities.createAnnotatedPluginDocument(document);
          imported.add(apd);
          return apd;
      }
  
      @Override
      public AnnotatedPluginDocument addDocument(AnnotatedPluginDocument annotatedDocument) {
          imported.add(annotatedDocument);
          return annotatedDocument;
      }
  };
  
  // Call the importers method directly and then add the results to the destination folder
  List<File> unused = importer.importDocumentsFromMultipleFilesReturningUnimported(importerP.getOptions(files, ProgressListener.EMPTY), files, callback, ProgressListener.EMPTY);
  for (AnnotatedPluginDocument toAdd : imported) {
      destination.addDocumentCopy(toAdd, ProgressListener.EMPTY);
  }

   

   

  0
• 

  Dave OConnor

  • September 25, 2025 22:29

  Thanks - this got me unstuck and its working now!

  0

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