本文整理汇总了C++中Sequence::get_iterator方法的典型用法代码示例。如果您正苦于以下问题：C++ Sequence::get_iterator方法的具体用法？C++ Sequence::get_iterator怎么用？C++ Sequence::get_iterator使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Sequence的用法示例。
在下文中一共展示了Sequence::get_iterator方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: padded_alignment
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 {
//.........这里部分代码省略.........
示例2: dna
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();
//.........这里部分代码省略.........