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 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;
}