+ general_assert(record_val == 1 || hits.getNHits() == 0, "Read " + record_read.getName() + " is both unalignable and alignable according to the input SAM/BAM file!");
+
// flush out previous read's hits if the read is alignable reads
if (record_val == 1) {
hits.updateRI();
// flush out previous read's hits if the read is alignable reads
if (record_val == 1) {
hits.updateRI();
@@ -167,7+169,7 @@ int main(int argc, char* argv[]) {