@Override public void write(K ignored, VariantContextWritable vc) { writeRecord(vc.get()); } }
@Override public void write(K ignored, VariantContextWritable vc) { writeRecord(vc.get()); } }
@Override public void write(K ignored, VariantContextWritable vc) { writeRecord(vc.get()); } }
@Override public void write(K ignored, VariantContextWritable vc) { writeRecord(vc.get()); } }
@Override public void write(K ignored, VariantContextWritable vc) { writeRecord(vc.get()); } }
@Override public void write(K ignored, VariantContextWritable vc) { writeRecord(vc.get()); } }
public void checkReading(ValidationStringency validationStringency) throws Exception { String filename = "invalid_info_field.vcf"; Configuration conf = new Configuration(); String input_file = ClassLoader.getSystemClassLoader().getResource(filename).getFile(); conf.set("mapred.input.dir", "file://" + input_file); if (validationStringency != null) { VCFRecordReader.setValidationStringency(conf, validationStringency); } TaskAttemptContext taskAttemptContext = new TaskAttemptContextImpl(conf, mock(TaskAttemptID.class)); JobContext ctx = new JobContextImpl(conf, taskAttemptContext.getJobID()); VCFInputFormat inputFormat = new VCFInputFormat(conf); List<InputSplit> splits = inputFormat.getSplits(ctx); assertEquals(1, splits.size()); RecordReader<LongWritable, VariantContextWritable> reader = inputFormat.createRecordReader(splits.get(0), taskAttemptContext); int counter = 0; while (reader.nextKeyValue()) { VariantContextWritable writable = reader.getCurrentValue(); assertNotNull(writable); VariantContext vc = writable.get(); assertNotNull(vc); String value = vc.toString(); assertNotNull(value); counter++; } assertEquals(4, counter); }
writable.readFields(new DataInputStream(bis)); VariantContext vc = writable.get(); Assert.assertArrayEquals("comparing Alleles",ctx.getAlleles().toArray(),vc.getAlleles().toArray()); Assert.assertEquals("comparing Log10PError",ctx.getLog10PError(),vc.getLog10PError(),0.01);
@Test public void countEntries() throws Exception { VCFFileReader vcfFileReader = new VCFFileReader(new File("src/test/resources/" + filename), false); Iterator<VariantContext> variantIterator; if (interval == null) { variantIterator = vcfFileReader.iterator(); } else { variantIterator = vcfFileReader.query(interval.getContig(), interval.getStart(), interval.getEnd()); } int expectedCount = Iterators.size(variantIterator); int counter = 0; for (RecordReader<LongWritable, VariantContextWritable> reader : readers) { while (reader.nextKeyValue()) { writable = reader.getCurrentValue(); assertNotNull(writable); VariantContext vc = writable.get(); assertNotNull(vc); String value = vc.toString(); assertNotNull(value); counter++; } } assertEquals(expectedCount, counter); }