@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 countRecordsInQueryInterval(final SamReader reader, final QueryInterval query) {
final SAMRecordIterator iter = reader.queryOverlapping(new QueryInterval[] {query});
int count = 0;
while (iter.hasNext()) {
iter.next();
count++;
}
iter.close();
return count;
}
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 countAlignmentsInWindow(
int reference, int window, SAMFileReader reader, int expectedCount) {
final int SIXTEEN_K = 1 << 14; // 1 << LinearIndex.BAM_LIDX_SHIFT
final int start = window >> 14; // window * SIXTEEN_K;
final int stop = ((window + 1) >> 14) - 1; // (window + 1 * SIXTEEN_K) - 1;
final String chr = reader.getFileHeader().getSequence(reference).getSequenceName();
// get records for the entire linear index window
SAMRecordIterator iter = reader.queryOverlapping(chr, start, stop);
SAMRecord rec;
int count = 0;
while (iter.hasNext()) {
rec = iter.next();
count++;
if (expectedCount == -1) System.err.println(rec.getReadName());
}
iter.close();
return count;
}
@Test(dataProvider = "composeAllPermutationsOfSamInputResource")
public void queryInputResourcePermutation(final SamInputResource resource) throws IOException {
final SamReader reader = SamReaderFactory.makeDefault().open(resource);
LOG.info(String.format("Query from %s ...", resource));
if (reader.hasIndex()) {
final StopWatch stopWatch = new StopWatch();
stopWatch.start();
final SAMRecordIterator q1 = reader.query("chr1", 500000, 100000000, true);
observedRecordOrdering1.add(Iterables.slurp(q1));
q1.close();
final SAMRecordIterator q20 = reader.query("chr20", 1, 1000000, true);
observedRecordOrdering20.add(Iterables.slurp(q20));
q20.close();
final SAMRecordIterator q3 = reader.query("chr3", 1, 10000000, true);
observedRecordOrdering3.add(Iterables.slurp(q3));
q3.close();
stopWatch.stop();
LOG.info(String.format("Finished queries in %sms", stopWatch.getElapsedTime()));
Assert.assertEquals(
observedRecordOrdering1.size(), 1, "read different records for chromosome 1");
Assert.assertEquals(
observedRecordOrdering20.size(), 1, "read different records for chromosome 20");
Assert.assertEquals(
observedRecordOrdering3.size(), 1, "read different records for chromosome 3");
} else if (resource.indexMaybe() != null) {
LOG.warn("Resource has an index source, but is not indexed: " + resource);
} else {
LOG.info("Skipping query operation: no index.");
}
reader.close();
}
