@Test public void testReadStartInMiddle() throws IOException { writeToTempQseq(twoQseq); split = new FileSplit(new Path(tempQseq.toURI().toString()), 10, twoQseq.length() - 10, null); QseqRecordReader reader = new QseqRecordReader(conf, split); assertEquals(oneQseq.length() + 1, reader.getPos()); // The start of the second record. We +1 for the \n that is not in oneQseq assertEquals(0.0, reader.getProgress(), 0.01); boolean retval = reader.next(key, fragment); assertTrue(retval); assertEquals("ERR020229:10883:1:1:1796:2044:2", key.toString()); assertEquals("TGAGCAGATGTGCTAAAGCTGCTTCTCCCCTAGGATCATTTGTACCTACCAGACTCAGGGAAAGGGGTGAGAATTGGGCCGTGGGGCAAGG", fragment.getSequence().toString()); assertEquals("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%", fragment.getQuality().toString()); assertEquals(twoQseq.length(), reader.getPos()); // now should be at the end of the data assertEquals(1.0, reader.getProgress(), 0.01); retval = reader.next(key, fragment); assertFalse(retval); }
@Test public void testReadFromStart() throws IOException { QseqRecordReader reader = createReaderForOneQseq(); assertEquals(0, reader.getPos()); assertEquals(0.0, reader.getProgress(), 0.01); boolean retval = reader.next(key, fragment); assertTrue(retval); //System.err.println("in testReadFromStart quality: " + fragment.getQuality().toString()); assertEquals("ERR020229:10880:1:1:1373:2042:1", key.toString()); assertEquals("TTGGATGATAGGGATTATTTGACTCGAATATTGGAAATAGCTGTTTATATTTTTTAAAAATGGTCTGTAACTGGTGACAGGACGCTTCGAT", fragment.getSequence().toString()); assertEquals("###########################################################################################", fragment.getQuality().toString()); assertEquals(oneQseq.length(), reader.getPos()); assertEquals(1.0, reader.getProgress(), 0.01); retval = reader.next(key, fragment); assertFalse(retval); }