public static File.Bioformat detectBioformat(URI uri) { return detectBioformat(uri, detectFormat(uri), detectCompression(uri)); }
File.Format format = FileUtils.detectFormat(fileUri); File.Bioformat bioformat = FileUtils.detectBioformat(fileUri);
public static VariantFileMetadata readVariantFileMetadata(File file, URI fileUri) throws IOException { File.Format format = file.getFormat(); File.Format detectFormat = FileUtils.detectFormat(fileUri); if (format == File.Format.VCF || format == File.Format.GVCF || format == File.Format.BCF || detectFormat == File.Format.VCF || detectFormat == File.Format.GVCF || detectFormat == File.Format.BCF) { VariantFileMetadata metadata = new VariantFileMetadata(String.valueOf(file.getUid()), file.getName()); metadata.setId(String.valueOf(file.getUid())); return VariantMetadataUtils.readVariantFileMetadata(Paths.get(fileUri.getPath()), metadata); } else { return null; } }
public static AlignmentHeader readAlignmentHeader(Study study, File file, URI fileUri) { if (file.getFormat() == File.Format.SAM || file.getFormat() == File.Format.BAM || FileUtils.detectFormat(fileUri) == File.Format.SAM || FileUtils.detectFormat(fileUri) == File.Format.BAM) { AlignmentSamDataReader reader = new AlignmentSamDataReader(Paths.get(fileUri), study.getName()); try { reader.open(); reader.pre(); reader.post(); // reader.getSamHeader().get return reader.getHeader(); } finally { reader.close(); } } else { return null; } }
File.Format format = FileUtils.detectFormat(fileUri);