bool Realigner::CreateRefFromQueryBases(
// Inputs:
const string& algn_query_bases,
const vector<CigarOp>& algn_cigar_data,
const string& md_tag,
const bool clip_anchors)
{
// Step 1. Generate reference sequence based on QueryBases and Cigar alone
if (verbose_) {
cout << "Original Cigar : ";
for (vector<CigarOp>::const_iterator cigar = algn_cigar_data.begin(); cigar != algn_cigar_data.end(); ++cigar)
cout << cigar->Length << cigar->Type;
cout << endl << "Original MD tag: " << md_tag << endl;
}
// Initialize variables
pretty_tseq_.clear();
pretty_qseq_.clear();
pretty_aln_.clear();
q_seq_.clear();
t_seq_.clear();
clipped_anchors_.cigar_left.resize(1);
clipped_anchors_.cigar_left[0].Type = 'S';
clipped_anchors_.cigar_left[0].Length = 0;
clipped_anchors_.cigar_right.resize(1);
clipped_anchors_.cigar_right[0].Type = 'S';
clipped_anchors_.cigar_right[0].Length = 0;
clipped_anchors_.md_left.clear();
clipped_anchors_.md_right.clear();
const char *read_ptr = algn_query_bases.c_str();
for (vector<CigarOp>::const_iterator cigar = algn_cigar_data.begin(); cigar != algn_cigar_data.end(); ++cigar) {
switch (cigar->Type) {
case ('M') :
case ('=') :
case ('X') :
t_seq_.append(read_ptr, cigar->Length);
q_seq_.append(read_ptr, cigar->Length);
pretty_tseq_.append(read_ptr, cigar->Length);
pretty_qseq_.append(read_ptr, cigar->Length);
pretty_aln_.append(cigar->Length, '|');
read_ptr += cigar->Length; break;
case ('I') :
q_seq_.append(read_ptr, cigar->Length);
pretty_tseq_.append(cigar->Length,'-');
pretty_qseq_.append(read_ptr, cigar->Length);
pretty_aln_.append(cigar->Length, '+');
read_ptr += cigar->Length; break;
case ('S') :
read_ptr += cigar->Length;
if (cigar == algn_cigar_data.begin())
clipped_anchors_.cigar_left[0].Length = cigar->Length;
else if (cigar == algn_cigar_data.end()-1)
clipped_anchors_.cigar_right[0].Length = cigar->Length;
else {
if (verbose_)
cout << "Error: invalid cigar string with soft clipped bases in the middle in the input." << endl;
return false;
}
break;
case ('D') :
case ('P') :
case ('N') :
t_seq_.append(cigar->Length, '-');
pretty_tseq_.append(cigar->Length,'-');
pretty_qseq_.append(cigar->Length,'-');
pretty_aln_.append(cigar->Length, '-');
break;
}
}
// Step 2: Further patch the sequence based on MD tag
unsigned int t_idx = 0;
unsigned int md_idx = 0;
unsigned int pretty_idx = 0;
int item_length = 0;
while (md_idx < md_tag.length()) {
if (md_tag.at(md_idx) >= '0' and md_tag.at(md_idx) <='9') { // it's a match
item_length = 0;
for (; md_idx < md_tag.length() and md_tag.at(md_idx) >= '0' and md_tag.at(md_idx) <= '9'; md_idx++)
item_length = 10*item_length + md_tag.at(md_idx) - '0';
t_idx += item_length;
while (pretty_idx < pretty_aln_.length() and (item_length > 0 or pretty_aln_.at(pretty_idx) == '+')) {
if (pretty_aln_[pretty_idx] != '+')
item_length--;
pretty_idx++;
}
}
else {
bool is_deletion = false;
if (md_tag.at(md_idx) == '^') { // Its a deletion or substitution
md_idx++;
is_deletion = true;
}
while (t_idx < t_seq_.length() and md_idx < md_tag.length() and pretty_idx < pretty_tseq_.length() and
md_tag.at(md_idx) >= 'A' and md_tag.at(md_idx) <= 'Z') {
if (pretty_aln_[pretty_idx] == '|') {
if (is_deletion) {
invalid_cigar_in_input = true;
return false;
}
pretty_aln_[pretty_idx] = ' ';
}
pretty_tseq_[pretty_idx++] = md_tag.at(md_idx) + 'a' - 'A';
t_seq_.at(t_idx) = md_tag.at(md_idx);
t_idx++;
md_idx++;
}
}
// Checks if Cigar and MD tag are consistent with each other
bool invalid_pair = item_length > 0;
invalid_pair = invalid_pair or (t_idx > t_seq_.length());
invalid_pair = invalid_pair or (pretty_idx == pretty_aln_.length() and md_idx < md_tag.length()-1);
invalid_pair = invalid_pair or (md_idx == md_tag.length() and t_idx != t_seq_.length());
invalid_pair = invalid_pair or (md_idx == md_tag.length() and pretty_idx != pretty_aln_.length());
if (invalid_pair) {
invalid_cigar_in_input = true;
return false;
}
}
// ------------------------------------------------ */
if (verbose_) {
cout << "Original Alignment from BAM: " << endl << pretty_qseq_ << endl;
cout << pretty_aln_ << endl << pretty_tseq_ << endl << endl;
}
// Step 3: Decide whether to realign this read and whether to clip ends
bool realign_read = ClipAnchors(clip_anchors);
if (realign_read)
SetSequences(q_seq_, t_seq_, pretty_aln_, isForwardStrandRead_);
return realign_read;
}
// prepare internal structures for clipping and alignment
// returns true if realignment was performed
bool RealignImp::compute_alignment (
const char* q_seq,
unsigned q_len,
const char* r_seq,
unsigned r_len,
int r_pos,
bool forward,
const uint32_t* cigar,
unsigned cigar_sz,
uint32_t*& cigar_dest,
unsigned& cigar_dest_sz,
int& new_pos,
bool& already_perfect,
bool& clip_failed,
bool& alignment_failed,
bool& unclip_failed)
{
already_perfect = false;
alignment_failed = false;
unclip_failed = false;
unsigned oplen;
const char* q_seq_clipped = q_seq;
const uint32_t* cigar_clipped = cigar;
unsigned cigar_sz_clipped = cigar_sz;
unsigned sclip_q_len, sclip_r_len, sclip_al_len;
assert (cigar_sz);
// reset realigner
Reset ();
// set clipping
SetClipping ((int) cliptype_, forward);
// clip out the hard and soft clipping zones from 5" and 3"
// The 'cut out' of the q_seq is done by switching to downstream pointer.
if (bam_cigar_op (*cigar) == BAM_CSOFT_CLIP)
{
oplen = bam_cigar_oplen (*cigar);
ClipStart (oplen);
q_seq_clipped += oplen;
++cigar_clipped;
--cigar_sz_clipped;
}
if (cigar_sz > 1 && bam_cigar_op (cigar [cigar_sz - 1]) == BAM_CSOFT_CLIP)
{
oplen = bam_cigar_oplen (cigar [cigar_sz - 1]);
ClipEnd (oplen);
--cigar_sz_clipped;
}
// cigar defines q_seq and t_seq lengths
sclip_al_len = seq_lens_from_bin_cigar (cigar_clipped, cigar_sz_clipped, &sclip_q_len, &sclip_r_len);
const std::string query (q_seq_clipped, sclip_q_len);
const std::string target (r_seq, sclip_r_len);
std::string pretty_al; pretty_al.reserve (sclip_al_len);
pretty_al_from_bin_cigar (cigar_clipped, cigar_sz_clipped, q_seq_clipped, r_seq, pretty_al);
// Realigner requires strings of proper size to be passed to SetSequences
SetSequences (query, target, pretty_al, forward);
if (!ClipAnchors (clip_failed))
{
already_perfect = true;
return false; // alignment already good, no imperfect zone to realign found
}
// TODO avoid automatic vectors to prevent unneeded heap usage
vector<MDelement> new_md_vec;
vector<CigarOp> new_cigar_vec;
unsigned int start_pos_shift;
if (!computeSWalignment(new_cigar_vec, new_md_vec, start_pos_shift))
{
alignment_failed = true;
return false;
}
if (!addClippedBasesToTags(new_cigar_vec, new_md_vec, q_len))
{
unclip_failed = true;
return false; // error adding back clipped out zones
}
if (!LeftAnchorClipped () && start_pos_shift != 0)
{
// build cigar data only if it is needed
// TODO avoid automatic vectors to prevent unneeded heap usage
std::vector <CigarOp> cigar_vec;
cigar_vector_from_bin (cigar, cigar_sz, cigar_vec);
new_pos = updateReadPosition (cigar_vec, start_pos_shift, r_pos);
}
else
new_pos = r_pos;
// free (cigar_dest);
// TODO: switch to better alignment memory management, avoid heap operations
cigar_dest = (uint32_t*) tmap_malloc (sizeof (uint32_t) * new_cigar_vec.size (), "cigar_dest");
cigar_dest_sz = new_cigar_vec.size ();
cigar_vector_to_bin (new_cigar_vec, cigar_dest);
return true;
}
