本文整理汇总了C++中Mapping::is_reverse方法的典型用法代码示例。如果您正苦于以下问题：C++ Mapping::is_reverse方法的具体用法？C++ Mapping::is_reverse怎么用？C++ Mapping::is_reverse使用的例子？那么, 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Mapping的用法示例。
在下文中一共展示了Mapping::is_reverse方法的1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: compute_from_edit
void Pileups::compute_from_edit(NodePileup& pileup, int64_t& node_offset,
int64_t& read_offset,
const Node& node, const Alignment& alignment,
const Mapping& mapping, const Edit& edit) {
string seq = edit.sequence();
bool is_reverse = mapping.is_reverse();
// ***** MATCH *****
if (edit.from_length() == edit.to_length()) {
assert (edit.from_length() > 0);
make_match(seq, edit.from_length(), is_reverse);
assert(seq.length() == edit.from_length());
int64_t delta = is_reverse ? -1 : 1;
for (int64_t i = 0; i < edit.from_length(); ++i) {
BasePileup* base_pileup = get_create_base_pileup(pileup, node_offset);
// reference_base if empty
if (base_pileup->num_bases() == 0) {
base_pileup->set_ref_base(node.sequence()[node_offset]);
} else {
assert(base_pileup->ref_base() == node.sequence()[node_offset]);
}
// add base to bases field (converting to ,. if match)
char base = seq[i];
if (!edit.sequence().empty() &&
base_equal(seq[i], node.sequence()[node_offset], is_reverse)) {
base = is_reverse ? ',' : '.';
}
*base_pileup->mutable_bases() += base;
// add quality if there
if (!alignment.quality().empty()) {
*base_pileup->mutable_qualities() += alignment.quality()[read_offset];
}
// pileup size increases by 1
base_pileup->set_num_bases(base_pileup->num_bases() + 1);
// move right along read, and left/right depending on strand on reference
node_offset += delta;
++read_offset;
}
}
// ***** INSERT *****
else if (edit.from_length() < edit.to_length()) {
make_insert(seq, is_reverse);
assert(edit.from_length() == 0);
// we define insert (like sam) as insertion between current and next
// position (on forward node coordinates). this means an insertion before
// offset 0 is invalid!
int64_t insert_offset = is_reverse ? node_offset : node_offset - 1;
if (insert_offset >= 0) {
BasePileup* base_pileup = get_create_base_pileup(pileup, insert_offset);
// reference_base if empty
if (base_pileup->num_bases() == 0) {
base_pileup->set_ref_base(node.sequence()[insert_offset]);
} else {
assert(base_pileup->ref_base() == node.sequence()[insert_offset]);
}
// add insertion string to bases field
// todo: should we reverse complement this if mapping is reversed ???
base_pileup->mutable_bases()->append(seq);
if (!alignment.quality().empty()) {
*base_pileup->mutable_qualities() += alignment.quality()[read_offset];
}
// pileup size increases by 1
base_pileup->set_num_bases(base_pileup->num_bases() + 1);
}
else {
// todo: need to either forget about these, or extend pileup format.
// easy solution: change insert to come before position, and just add
// optional pileup at n+1st base of node. would like to figure out
// how samtools does it first...
/*
stringstream ss;
ss << "Warning: pileup does not support insertions before 0th base in node."
<< " Offending edit: " << pb2json(edit) << endl;
#pragma omp critical(cerr)
cerr << ss.str();
*/
}
// move right along read (and stay put on reference)
read_offset += edit.to_length();
}
// ***** DELETE *****
else {
assert(edit.to_length() == 0);
assert(edit.sequence().empty());
int64_t del_start = !is_reverse ? node_offset :
node_offset - edit.from_length() + 1;
seq = node.sequence().substr(del_start, edit.from_length());
make_delete(seq, is_reverse);
BasePileup* base_pileup = get_create_base_pileup(pileup, node_offset);
// reference_base if empty
if (base_pileup->num_bases() == 0) {
base_pileup->set_ref_base(node.sequence()[node_offset]);
} else {
assert(base_pileup->ref_base() == node.sequence()[node_offset]);
}
// add deletion string to bases field
// todo: should we reverse complement this if mapping is reversed ???
base_pileup->mutable_bases()->append(seq);
if (!alignment.quality().empty()) {
*base_pileup->mutable_qualities() += alignment.quality()[read_offset];
//.........这里部分代码省略.........