@Exec
public void exec() throws IOException, CommandArgumentException {
if (filename == null) {
throw new CommandArgumentException("You must specify an input BAM filename!");
}
SamReaderFactory readerFactory = SamReaderFactory.makeDefault();
if (lenient) {
readerFactory.validationStringency(ValidationStringency.LENIENT);
} else if (silent) {
readerFactory.validationStringency(ValidationStringency.SILENT);
}
SamReader reader = null;
String name;
FileChannel channel = null;
if (filename.equals("-")) {
reader = readerFactory.open(SamInputResource.of(System.in));
name = "<stdin>";
} else {
File f = new File(filename);
FileInputStream fis = new FileInputStream(f);
channel = fis.getChannel();
reader = readerFactory.open(SamInputResource.of(fis));
name = f.getName();
}
Iterator<SAMRecord> it =
ProgressUtils.getIterator(
name,
reader.iterator(),
(channel == null) ? null : new FileChannelStats(channel),
new ProgressMessage<SAMRecord>() {
long i = 0;
@Override
public String msg(SAMRecord current) {
i++;
return i + " " + current.getReadName();
}
},
new CloseableFinalizer<SAMRecord>());
long i = 0;
while (it.hasNext()) {
i++;
it.next();
}
reader.close();
System.err.println("Successfully read: " + i + " records.");
}
public void close() throws IOException {
if (reader != null) {
reader.close();
}
}