public void testEmptyFastq() throws IOException {
final SequencesReader reader = ReaderTestUtils.getReaderDNAFastq("", mDir, false);
reader.close();
final CompressedMemorySequencesReader cmsr =
new CompressedMemorySequencesReader(
mDir, new IndexFile(mDir), 5, true, false, new LongRange(0, 0));
assertEquals(0, cmsr.numberSequences());
}
@Override
public void testEquals() throws IOException {
final File dir = FileHelper.createTempDirectory(mDir);
final File otherDir = FileHelper.createTempDirectory(mDir);
ReaderTestUtils.getReaderDNAFastq("", dir, false).close();
ReaderTestUtils.getReaderDNAFastq("", otherDir, false).close();
final CompressedMemorySequencesReader cmsr =
new CompressedMemorySequencesReader(
dir, new IndexFile(dir), 5, true, false, new LongRange(0, 0));
final CompressedMemorySequencesReader other =
new CompressedMemorySequencesReader(
otherDir, new IndexFile(dir), 5, true, false, new LongRange(0, 0));
assertTrue(cmsr.equals(cmsr));
assertFalse(cmsr.equals(null));
assertFalse(cmsr.equals(other));
assertFalse(cmsr.equals("FDSA"));
}
public void testOverEndFastq() throws Exception {
final SequencesReader reader = ReaderTestUtils.getReaderDNAFastq(POSITIONS_FASTQ, mDir, false);
reader.close();
new CompressedMemorySequencesReader(
mDir, new IndexFile(mDir), 5, true, false, new LongRange(3, 8));
// Now this is OK rather than Exception, since our std behaviour is to warn and clip end that
// are too high back to the available num seqs
}
public void testFastqEnd() throws Exception {
final SequencesReader reader =
ReaderTestUtils.getReaderDNAFastq(POSITIONS_FASTQ, mDir, 20, false);
reader.close();
final SequencesIterator cmsr =
new CompressedMemorySequencesReader(
mDir, new IndexFile(mDir), 5, true, false, new LongRange(5, 6))
.iterator();
cmsr.nextSequence();
checkFastq(cmsr, "r5", "ACGTAC");
assertFalse(cmsr.nextSequence());
}
public void testRanges() throws Exception {
final SequencesReader reader = ReaderTestUtils.getReaderDNAFastq(SMALL_FASTQ, mDir, 20, false);
reader.close();
final CompressedMemorySequencesReader cmsr =
new CompressedMemorySequencesReader(
mDir, new IndexFile(mDir), 5, true, false, LongRange.NONE);
final byte[] foo = new byte[6];
cmsr.readQuality(0, foo, 4, 6);
final String qual = "EFGHIJ";
for (int i = 0; i < foo.length; i++) {
assertEquals(qual.charAt(i) - '!', foo[i]);
}
}
