void BAMUtils::padded_alignment() {
Cigar cig = bam_record.get_cigar();
Sequence tdna = bam_record.get_seq();
int sdna_pos = 0;
int tdna_pos = 0;
pad_source.reserve(t_dna.length());
pad_target.reserve(t_dna.length());
pad_match.reserve(t_dna.length());
Sequence::iterator tdna_itr = tdna.get_iterator();
int tot = 0;
//find out if the first cigar op could be soft clipped or not
is_three_prime_soft_clipped = false;
for (Cigar::iterator i = cig.get_iterator(); i.good(); i.next()) {
//i.op(); i.len();
if (this->bam_record.mapped_reverse_strand()) {
if (tot > ( cig.get_length( ) - 3) ){
if (i.op() == 'S')
is_three_prime_soft_clipped = true;
else
is_three_prime_soft_clipped = false;
}
} else {
if (tot < 2) {
if (i.op() == 'S')
is_three_prime_soft_clipped = true;
else
is_three_prime_soft_clipped = false;
}
}
if (i.op() == 'I' ) {
pad_source.append(i.len(), '-');
int count = 0;
tdna_itr.set_position(tdna_pos);
while (tdna_itr.good()) {
if (count >= i.len()) {
break;
} else {
pad_target += tdna_itr.get();
tdna_itr.next();
tdna_pos++;
count++;
}
}
pad_match.append(i.len(), '+');
}
else if(i.op() == 'D' || i.op() == 'N') {
pad_source.append( t_dna.substr(sdna_pos, i.len()));
sdna_pos += i.len();
pad_target.append(i.len(), '-');
pad_match.append(i.len(), '-');
}
else if(i.op() == 'P') {
pad_source.append(i.len(), '*');
pad_target.append(i.len(), '*');
pad_match.append(i.len(), ' ');
} else if (i.op() == 'S') {
if (!truncate_soft_clipped) {
pad_source.append(i.len(), '-');
pad_match.append(i.len(), '+');
pad_target.append(i.len(), '+');
}
int count = 0;
while (tdna_itr.good()) {
if (count >= i.len()) {
break;
}
tdna_pos++;
tdna_itr.next();
count++;
}
}
else if (i.op() == 'H') {
//nothing for clipped bases
}else {
std::string ps, pt, pm;
ps.reserve(i.len());
pm.reserve(i.len());
ps = t_dna.substr(sdna_pos,i.len()); //tdna is really qdna
tdna_itr.set_position(tdna_pos);
int count = 0;
while (tdna_itr.good()) {
if (count < i.len()) {
pt += tdna_itr.get();
} else {
break;
}
tdna_itr.next();
count++;
}
for (unsigned int z = 0; z < ps.length(); z++) {
if (ps[z] == pt[z]) {
pad_match += '|';
} else if (ps[z] != 'A' || ps[z] != 'C' || ps[z] != 'G' || ps[z] != 'T') {
if (iupac_flag) {
std::vector<char> nukes(IUPAC::get_base(ps[z]));
bool replaced = false;
unsigned int nuke_ptr = 0;
for (unsigned int n = 0; n < nukes.size(); n++) {
if (nukes[n] == pt[z]) {
pad_match += '|';
replaced = true;
nuke_ptr = n;
break;
}
//nuke_ptr++;
}
if (!replaced) {
pad_match += ' ';
}
else if (!keep_iupac) {
//std::cerr << "nukes["<<nuke_ptr<<"]: " << nukes[nuke_ptr] << " nukes.size() " << nukes.size() << std::endl;
ps[z] = nukes[nuke_ptr];
}//keep_iupac
}//iupac_flag
else {
pad_match += ' ';
}
}//end else if checking ps[z] agianst nukes
else {
pad_match += ' ';
}
}//end for loop
pad_source += ps;
pad_target += pt;
sdna_pos += i.len();
tdna_pos += i.len();
}
tot++;
}
/*
std::cerr << "pad_source: " << pad_source << std::endl;
std::cerr << "pad_target: " << pad_target << std::endl;
std::cerr << "pad_match : " << pad_match << std::endl;
*/
}
void BAMUtils::dna() {
MD md = bam_record.get_md();
Cigar cig = bam_record.get_cigar();
Sequence qseq = bam_record.get_seq();
int position = 0;
std::string seq;
Sequence::iterator qseq_itr = qseq.get_iterator();
for (Cigar::iterator i = cig.get_iterator(); i.good(); i.next()) {
if (i.op() == 'M') {
int count = 0;
while (qseq_itr.good()) {
if (count >= i.len()) {
break;
} else {
seq += qseq_itr.get();
qseq_itr.next();
count++;
}
}
} else if ((i.op() == 'I') || (i.op() == 'S')) {
int count = 0;
while (qseq_itr.good()) {
if (count >= i.len()) {
break;
}
qseq_itr.next();
count++;
}
//bool is_error = false;
if (i.op() == 'S') {
soft_clipped_bases += i.len();
//is_error = true;
}
}
position++;
}
t_dna.reserve(seq.length());
int start = 0;
MD::iterator md_itr = md.get_iterator();
std::string num;
coord_t md_len = 0;
char cur;
while (md_itr.good()) {
cur = md_itr.get();
if (std::isdigit(cur)) {
num+=cur;
//md_itr.next();
}
else {
if (num.length() > 0) {
md_len = convert(num);
num.clear();
t_dna += seq.substr(start, md_len);
start += md_len;
}
}
if (cur == '^') {
//get nuc
md_itr.next();
char nuc = md_itr.get();
while (std::isalpha(nuc)) {
t_dna += nuc;
md_itr.next();
nuc = md_itr.get();
}
num += nuc; //it's a number now will
//lose this value if i don't do it here
//cur = nuc;
} else if (std::isalpha(cur)) {
t_dna += cur;
start++;
}
md_itr.next();
}
//clean up residual num if there is any
if (num.length() > 0) {
md_len = convert(num);
num.clear();
t_dna += seq.substr(start, md_len);
start += md_len;
}
}
