if (inputFile.getBioformat().equals(File.Bioformat.VARIANT)) { Path metaFile = outdir.resolve(inputFile.getName() + "." + VariantReaderUtils.METADATA_FILE_FORMAT_GZ); if (!metaFile.toFile().exists()) {
fileSolrModel.setBioformat(file.getBioformat().name());
file.setFormat(format); if (bioformat != File.Bioformat.NONE && !bioformat.equals(file.getBioformat())) { modifyParams.put(FileDBAdaptor.QueryParams.BIOFORMAT.key(), bioformat); file.setBioformat(bioformat);
assert (fileSolrModel.getType().equals(file.getType().name())); assert (fileSolrModel.getFormat().equals(file.getFormat().name())); assert (fileSolrModel.getBioformat().equals(file.getBioformat().name())); assert (fileSolrModel.getRelease() == file.getRelease());
private void checkAlignmentBioformat(File file) throws CatalogException { if (!file.getBioformat().equals(File.Bioformat.ALIGNMENT)) { throw new CatalogException("File " + file.getName() + " not supported. Expecting an alignment file."); } }
private void checkAlignmentBioformat(List<FileInfo> fileInfo) throws CatalogException { for (FileInfo file : fileInfo) { if (!file.getBioformat().equals(File.Bioformat.ALIGNMENT)) { throw new CatalogException("File " + file.getName() + " not supported. Expecting an alignment file."); } } }