@Test
public void testBamIntegers() throws IOException {
final List<String> errorMessages = new ArrayList<String>();
final SamReader bamReader = SamReaderFactory.makeDefault().open(BAM_INPUT);
final File bamOutput = File.createTempFile("test", ".bam");
final File samOutput = File.createTempFile("test", ".sam");
final SAMFileWriter samWriter =
new SAMFileWriterFactory().makeWriter(bamReader.getFileHeader(), true, samOutput, null);
final SAMFileWriter bamWriter =
new SAMFileWriterFactory().makeWriter(bamReader.getFileHeader(), true, bamOutput, null);
final SAMRecordIterator iterator = bamReader.iterator();
while (iterator.hasNext()) {
try {
final SAMRecord rec = iterator.next();
samWriter.addAlignment(rec);
bamWriter.addAlignment(rec);
} catch (final Throwable e) {
System.out.println(e.getMessage());
errorMessages.add(e.getMessage());
}
}
CloserUtil.close(bamReader);
samWriter.close();
bamWriter.close();
Assert.assertEquals(errorMessages.size(), 0);
bamOutput.deleteOnExit();
samOutput.deleteOnExit();
}
private int countRecords(final SamReader reader) {
int count = 0;
try (final SAMRecordIterator iter = reader.iterator()) {
while (iter.hasNext()) {
iter.next();
count++;
}
}
return count;
}
private int runQueryTest(
final URL bamURL,
final String sequence,
final int startPos,
final int endPos,
final boolean contained) {
verbose("Testing query " + sequence + ":" + startPos + "-" + endPos + " ...");
final SamReader reader1 =
SamReaderFactory.makeDefault()
.disable(SamReaderFactory.Option.EAGERLY_DECODE)
.open(SamInputResource.of(bamURL).index(BAM_INDEX_FILE));
final SamReader reader2 =
SamReaderFactory.makeDefault()
.disable(SamReaderFactory.Option.EAGERLY_DECODE)
.open(SamInputResource.of(bamURL).index(BAM_INDEX_FILE));
final Iterator<SAMRecord> iter1 = reader1.query(sequence, startPos, endPos, contained);
final Iterator<SAMRecord> iter2 = reader2.iterator();
// Compare ordered iterators.
// Confirm that iter1 is a subset of iter2 that properly filters.
SAMRecord record1 = null;
SAMRecord record2 = null;
int count1 = 0;
int count2 = 0;
int beforeCount = 0;
int afterCount = 0;
while (true) {
if (record1 == null && iter1.hasNext()) {
record1 = iter1.next();
count1++;
}
if (record2 == null && iter2.hasNext()) {
record2 = iter2.next();
count2++;
}
// System.out.println("Iteration:");
// System.out.println(" Record1 = " + ((record1 == null) ? "null" : record1.format()));
// System.out.println(" Record2 = " + ((record2 == null) ? "null" : record2.format()));
if (record1 == null && record2 == null) {
break;
}
if (record1 == null) {
checkPassesFilter(false, record2, sequence, startPos, endPos, contained);
record2 = null;
afterCount++;
continue;
}
assertNotNull(record2);
final int ordering = compareCoordinates(record1, record2);
if (ordering > 0) {
checkPassesFilter(false, record2, sequence, startPos, endPos, contained);
record2 = null;
beforeCount++;
continue;
}
assertTrue(ordering == 0);
checkPassesFilter(true, record1, sequence, startPos, endPos, contained);
checkPassesFilter(true, record2, sequence, startPos, endPos, contained);
assertEquals(record1.getReadName(), record2.getReadName());
assertEquals(record1.getReadString(), record2.getReadString());
record1 = null;
record2 = null;
}
CloserUtil.close(reader1);
CloserUtil.close(reader2);
verbose("Checked " + count1 + " records against " + count2 + " records.");
verbose("Found " + (count2 - beforeCount - afterCount) + " records matching.");
verbose("Found " + beforeCount + " records before.");
verbose("Found " + afterCount + " records after.");
return count1;
}