bool less_than(bam1_t *a, bam1_t *b) {
int32_t ap1 = min(a->core.pos, a->core.mpos);
int32_t ap2 = max(a->core.pos, a->core.mpos);
int32_t bp1 = min(b->core.pos, b->core.mpos);
int32_t bp2 = max(b->core.pos, b->core.mpos);
bool less_than(bam1_t *a, bam1_t *b) {
int32_t ap1 = min(a->core.pos, a->core.mpos);
int32_t ap2 = max(a->core.pos, a->core.mpos);
int32_t bp1 = min(b->core.pos, b->core.mpos);
int32_t bp2 = max(b->core.pos, b->core.mpos);
if (isPaired) {
add_to_appropriate_arr(b);
while ((go_on = (samread(in, b) >= 0)) && (qname == bam1_qname(b))) {
if (isPaired) {
add_to_appropriate_arr(b);
while ((go_on = (samread(in, b) >= 0)) && (qname == bam1_qname(b))) {
- general_assert(arr_both.size() % 2 == 0, "Number of first and second mates in read " + qname + "'s full alignments (both mates are aligned) are not matched!", true);
- general_assert((arr_partial_1.size() + arr_partial_2.size() + arr_partial_unknown.size()) % 2 == 0, "Number of first and second mates in read " + qname + "'s partial alignments (at most one mate is aligned) are not matched!", true);
+ general_assert_1(arr_both.size() % 2 == 0, "Number of first and second mates in read " + qname + "'s full alignments (both mates are aligned) are not matched!");
+ general_assert_1((arr_partial_1.size() + arr_partial_2.size() + arr_partial_unknown.size()) % 2 == 0, "Number of first and second mates in read " + qname + "'s partial alignments (at most one mate is aligned) are not matched!");