@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;
}
