inline int32_t right() const {
if (isPaired()) {
return std::max(bam_pos(read1) + bam_seq_len(read1),
bam_pos(read2) + bam_seq_len(read2));
} else {
return bam_pos(read1) + bam_seq_len(read1);
}
}
inline uint32_t fragLen() const {
if (!isPaired()) { return 0; }
auto leftmost1 = bam_pos(read1);
auto leftmost2 = bam_pos(read2);
// The length of the mapped read that is "rightmost" w.r.t. the forward strand.
auto rightmostLen = (leftmost1 < leftmost2) ? bam_seq_len(read2) : bam_seq_len(read1);
return std::abs(leftmost1 - leftmost2) + rightmostLen;
//return std::abs(read1->core.isize) + std::abs(read1->core.l_qseq) + std::abs(read2->core.l_qseq);
}
inline int32_t right() { return left() + bam_seq_len(read); }
