bool
is_indel_conflict(const indel_key& ik1,
const indel_key& ik2) {
// add one to the end_pos of all indels to prevent immediately
// adjacent indels in the final alignments:
pos_range pr1(ik1.open_pos_range());
pr1.end_pos++;
pos_range pr2(ik2.open_pos_range());
pr2.end_pos++;
return pr1.is_range_intersect(pr2);
}
// 99% of this task is taking care of indel normalization
static
bool
convert_indel_to_htype(const indel_key& ik,
const indel_data& /*id*/,
const read_segment& rseg,
const reference_contig_segment& ref,
htype_element& he) {
he.clear();
// get best alignment:
const alignment* alptr(rseg.get_best_alignment());
assert(alptr);
const alignment& al(*alptr);
// Check that alignment is compatible with indel. Many
// cases where this fails will be for 'private'
// indels. The posterior above is over all candidate
// indels, so one candidate may be the best for this read,
// *but* the best alignment contains a private indel
// instead.
//
pos_range read_indel_pr;
if (! is_indel_in_alignment(al,ik,read_indel_pr)) return false;
const bam_seq read_seq(rseg.get_bam_read());
const rc_segment_bam_seq ref_bseq(ref);
pos_range ref_indel_pr(ik.open_pos_range());
assert(! read_indel_pr.is_empty());
assert(! ref_indel_pr.is_empty());
// normalization function adjusts ranges:
// normalize_indel(read_indel_pr,ref_indel_pr,read_seq,ref_bseq,read_indel_pr,ref_indel_pr);
assert(! read_indel_pr.is_empty());
assert(! ref_indel_pr.is_empty());
// build he:
if (ref_indel_pr.is_complete()) {
he.delete_length=ref_indel_pr.end_pos-ref_indel_pr.begin_pos;
}
if (! read_indel_pr.is_begin_pos) {
he.pos=read_indel_pr.end_pos;
} else {
he.pos=read_indel_pr.begin_pos;
}
if (! read_indel_pr.is_end_pos) {
he.open_end=OPEN::RIGHT;
} else if (! read_indel_pr.is_begin_pos) {
he.open_end=OPEN::LEFT;
}
{ // copy into htype element seq (don't worry about efficiency for now)
pos_range pr(read_indel_pr);
if (! pr.is_complete()) {
const pos_range nonclip_pr(get_nonclip_range(al.path));
assert(nonclip_pr.is_complete());
if (! pr.is_begin_pos) {
pr.set_begin_pos(nonclip_pr.begin_pos);
} else {
pr.set_end_pos(nonclip_pr.end_pos);
}
}
assert(pr.begin_pos<=pr.end_pos && pr.begin_pos>=0);
for (pos_t i(pr.begin_pos); i<pr.end_pos; ++i) {
he.seq.push_back(read_seq.get_char(i));
}
}
if ((he.delete_length==0) &&
(he.insert_length()==0)) {
he.clear();
return false;
}
return true;
}