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Merge pull request #55 from cartoonist/fix-warnings
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Fix warnings
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@edawson
edawson authored Jan 31, 2020
2 parents c5c006f + 2f6f189 commit d56b630
Showing 1 changed file with 24 additions and 23 deletions.
47 changes: 24 additions & 23 deletions src/gfakluge.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ namespace gfak{
else{
return -1;
}
};
}


// Provides the proper sorting behavior,
Expand Down Expand Up @@ -159,7 +159,7 @@ namespace gfak{
std::vector<bool> orientations;
std::vector<std::string> overlaps;
std::map<std::string, opt_elem> opt_fields;
};
}

/**
* Adds a GFA 0.1-style path_element (a "Walk") to a
Expand All @@ -173,7 +173,7 @@ namespace gfak{
segment_names.insert( segment_names.begin() + corrected_rank - 1, seg_name);
orientations.insert( orientations.begin() + corrected_rank - 1, ori);
overlaps.insert( overlaps.begin() + corrected_rank - 1, overlap);
};
}
/**
* Writes a path to a std::string in GFA1 format.
*/
Expand All @@ -199,7 +199,7 @@ namespace gfak{
std::string to_string_2() const{
std::ostringstream st;
std::vector<std::string> p_segs;
for (int i = 0; i < segment_names.size(); ++i){
for (size_t i = 0; i < segment_names.size(); ++i){
p_segs.push_back(segment_names[i] + (orientations[i] ? "+" : "-") );
}
st << "O" << '\t' << name << '\t' << pliib::join(p_segs, ",");
Expand Down Expand Up @@ -283,7 +283,7 @@ namespace gfak{
st << '>' << ' ' << name << std::endl
<< sequence;
return st.str();
};
}
};

/** Represents a link (a non-contained edge) between two sequence_elems
Expand Down Expand Up @@ -448,7 +448,7 @@ namespace gfak{
}
return st.str();
}
};
};

/** Represents a GAP type line ('G'), which is specific to GFA2 */
struct gap_elem{
Expand Down Expand Up @@ -708,10 +708,10 @@ namespace gfak{
std::map<std::string, std::vector<edge_elem> > seq_to_edges;
std::map<std::string, std::vector<gap_elem> > seq_to_gaps;
std::map<std::string, group_elem> groups;
};
}
~GFAKluge(){

};
}

inline double detect_version_from_file(const char* filename){
std::ifstream gfi;
Expand All @@ -738,7 +738,8 @@ namespace gfak{
header[h.key] = h;
}
}
};
}

inline void for_each_sequence_line_in_file(const char* filename, std::function<void(gfak::sequence_elem)> func){
std::ifstream gfi;
gfi.open(filename, std::ifstream::in);
Expand Down Expand Up @@ -808,7 +809,7 @@ namespace gfak{
header[h.key] = h;
}
}
};
}


inline void for_each_edge_line_in_file(char* filename, std::function<void(gfak::edge_elem)> func){
Expand Down Expand Up @@ -930,7 +931,7 @@ namespace gfak{
header[h.key] = h;
}
}
};
}



Expand All @@ -946,7 +947,7 @@ namespace gfak{
}
std::string line;
size_t i = 0;
bool seen_newline = true;
//bool seen_newline = true;
while (i < gfa_filesize) {
std::string path_name;
// scan forward
Expand Down Expand Up @@ -985,7 +986,7 @@ namespace gfak{
++i;
}
mmap_close(gfa_buf, gfa_fd, gfa_filesize);
};
}

/**
inline void for_each_path_line_in_file(const char* filename, std::function<void(gfak::path_elem)> func){
Expand Down Expand Up @@ -1104,7 +1105,7 @@ namespace gfak{
header[h.key] = h;
}
}
};
}

// Only supports GFA 2.0 style paths (i.e. groups, both ordered and unordered)
inline void for_each_ordered_group_line_in_file(const char* filename, std::function<void(gfak::group_elem)> func){
Expand Down Expand Up @@ -1154,7 +1155,7 @@ namespace gfak{
header[h.key] = h;
}
}
};
}


// GFAKluge does not, but maybe should, enforce graph structure,
Expand Down Expand Up @@ -1429,7 +1430,7 @@ namespace gfak{
// GFA2 getters
inline std::map<std::string, std::vector<edge_elem>> get_seq_to_edges(){
return seq_to_edges;
};
}
inline std::map<std::string, std::vector<fragment_elem>> get_seq_to_fragments(){
return seq_to_fragments;
}
Expand Down Expand Up @@ -1571,7 +1572,7 @@ namespace gfak{
}
this->one_compat = true;
}
};
}
// Wraps both gfa_1_ize() and gfa_2_ize()
inline void compatibilize(){
gfa_1_ize();
Expand Down Expand Up @@ -1980,7 +1981,7 @@ namespace gfak{
base_group_id = std::get<4>(new_mx);
std::uint64_t seg_diff = base_seq_id;
// Segments
int num_segs = name_to_seq.size();
//int num_segs = name_to_seq.size();

// locally cache name_to_seq,
// seq_to_edges, seq_to_fragments, groups,
Expand All @@ -2001,7 +2002,7 @@ namespace gfak{



uint64_t edge_count = 0;
//uint64_t edge_count = 0;
// Edges
for (auto e : seq_to_edges[old_name]){
e.source_name = ns.second.name;
Expand Down Expand Up @@ -2055,7 +2056,7 @@ namespace gfak{
inline void re_id(std::string new_mx_str){
std::vector<uint64_t> starts(5);
std::vector<std::string> starts_strs = pliib::split(new_mx_str, ':');
for (int i = 0; i < starts_strs.size(); ++i){
for (size_t i = 0; i < starts_strs.size(); ++i){
starts[i] = stoul(starts_strs[i]);
}
std::tuple<std::uint64_t, std::uint64_t, std::uint64_t, std::uint64_t, std::uint64_t> n_ids = std::make_tuple(starts[0], starts[1],
Expand Down Expand Up @@ -2251,7 +2252,7 @@ namespace gfak{
name_to_seq.erase(n_to_s);
graph_modified = true;
}
else if (minlen > 0 && s.length < minlen){
else if (minlen > 0 && s.length < (size_t)minlen){
dropped_seqs.insert(s.name);
name_to_seq.erase(n_to_s);
graph_modified = true;
Expand Down Expand Up @@ -2689,8 +2690,8 @@ namespace gfak{

return true;

};
}
};

};
}
#endif

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