public static File.Bioformat detectBioformat(URI uri) { return detectBioformat(uri, detectFormat(uri), detectCompression(uri)); }
@Test public void detectAlignment() { assertEquals(File.Bioformat.ALIGNMENT, FileUtils.detectBioformat(URI.create("file:///test.bam"))); assertEquals(File.Bioformat.ALIGNMENT, FileUtils.detectBioformat(URI.create("file:///test.sam"))); assertEquals(File.Bioformat.ALIGNMENT, FileUtils.detectBioformat(URI.create("file:///test.cram"))); assertEquals(File.Bioformat.ALIGNMENT, FileUtils.detectBioformat(URI.create("file:///test.sam.gz"))); assertEquals(File.Bioformat.ALIGNMENT, FileUtils.detectBioformat(URI.create("file:///test.bam.alignments.json"))); assertEquals(File.Bioformat.ALIGNMENT, FileUtils.detectBioformat(URI.create("file:///test.bam.alignments.json.gz"))); assertEquals(File.Bioformat.ALIGNMENT, FileUtils.detectBioformat(URI.create("file:///test.bam.alignments.json.snz"))); assertEquals(File.Bioformat.ALIGNMENT, FileUtils.detectBioformat(URI.create("file:///test.bam.alignments.avro"))); assertEquals(File.Bioformat.ALIGNMENT, FileUtils.detectBioformat(URI.create("file:///test.bam.alignments.avro.gz"))); assertEquals(File.Bioformat.ALIGNMENT, FileUtils.detectBioformat(URI.create("file:///test.bam.alignments.avro.snz"))); }
@Test public void detectSequence() { assertEquals(File.Bioformat.SEQUENCE, FileUtils.detectBioformat(URI.create("file:///test.fastq"))); assertEquals(File.Bioformat.SEQUENCE, FileUtils.detectBioformat(URI.create("file:///test.fastq.gz"))); }
File.Bioformat bioformat = FileUtils.detectBioformat(fileUri);
@Test public void detectPedigree() { assertEquals(File.Bioformat.PEDIGREE, FileUtils.detectBioformat(URI.create("file:///test.ped"))); assertEquals(File.Bioformat.PEDIGREE, FileUtils.detectBioformat(URI.create("file:///test.ped.gz"))); }
@Test public void detectVariant() { assertEquals(File.Bioformat.VARIANT, FileUtils.detectBioformat(URI.create("file:///test.vcf"))); assertEquals(File.Bioformat.VARIANT, FileUtils.detectBioformat(URI.create("file:///test.vcf.variants.json"))); assertEquals(File.Bioformat.VARIANT, FileUtils.detectBioformat(URI.create("file:///test.vcf.variants.json.gz"))); assertEquals(File.Bioformat.VARIANT, FileUtils.detectBioformat(URI.create("file:///test.vcf.gz"))); assertEquals(File.Bioformat.VARIANT, FileUtils.detectBioformat(URI.create("file:///test.vcf.gz.variants.json"))); assertEquals(File.Bioformat.VARIANT, FileUtils.detectBioformat(URI.create("file:///test.vcf.gz.variants.json.gz"))); assertEquals(File.Bioformat.VARIANT, FileUtils.detectBioformat(URI.create("file:///test.bcf"))); assertEquals(File.Bioformat.VARIANT, FileUtils.detectBioformat(URI.create("file:///test.bcf.variants.json"))); assertEquals(File.Bioformat.VARIANT, FileUtils.detectBioformat(URI.create("file:///test.bcf.variants.json.gz"))); assertEquals(File.Bioformat.VARIANT, FileUtils.detectBioformat(URI.create("file:///test.bcf.gz"))); assertEquals(File.Bioformat.VARIANT, FileUtils.detectBioformat(URI.create("file:///test.bcf.gz.variants.json"))); assertEquals(File.Bioformat.VARIANT, FileUtils.detectBioformat(URI.create("file:///test.bcf.gz.variants.json.gz"))); assertEquals(File.Bioformat.VARIANT, FileUtils.detectBioformat(URI.create("file:///test.bcf.gz.variants.json.snappy"))); assertEquals(File.Bioformat.VARIANT, FileUtils.detectBioformat(URI.create("file:///test.bcf.gz.variants.json.snz"))); assertEquals(File.Bioformat.NONE, FileUtils.detectBioformat(URI.create("file:///test.vcf.tbi"))); assertEquals(File.Bioformat.NONE, FileUtils.detectBioformat(URI.create("file:///test.vcf.txt"))); assertEquals(File.Bioformat.NONE, FileUtils.detectBioformat(URI.create("file:///test.vcf.json"))); }
File.Bioformat bioformat = FileUtils.detectBioformat(fileUri);