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Reduce complexity by reducing scope of some variables #79

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25 changes: 9 additions & 16 deletions ntedit.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1049,12 +1049,12 @@ writeEditsToFile(
if (snv_mode_no_edit) {
rfout << "\n";
}
unsigned curr_best_alt_supp = 0;
char best_alt_base = '1';
std::string best_alt_supp;
std::string genotype;
// If there are alt bases
if (!alt_base_vcf.empty()) {
unsigned curr_best_alt_supp = 0;
char best_alt_base = '1';
if (opt::snv) {
if (!snv_mode_no_edit) {
for (size_t i = 0; i < alt_base_vcf.size(); ++i) {
Expand Down Expand Up @@ -1567,12 +1567,6 @@ tryIndels(
{

// initialize temporary values
uint64_t temp_fhVal;
uint64_t temp_rhVal;
unsigned temp_h_seq_i;
unsigned temp_t_seq_i;
unsigned temp_h_node_index;
unsigned temp_t_node_index;
unsigned temp_best_num_support = 0;
unsigned temp_alt_num_support = 0;
std::string temp_best_indel;
Expand All @@ -1588,12 +1582,12 @@ tryIndels(
insertion_bases += draft_char;

// set temporary values
temp_fhVal = fhVal;
temp_rhVal = rhVal;
temp_h_seq_i = h_seq_i;
temp_t_seq_i = t_seq_i;
temp_h_node_index = h_node_index;
temp_t_node_index = t_node_index;
uint64_t temp_fhVal = fhVal;
uint64_t temp_rhVal = rhVal;
unsigned temp_h_seq_i = h_seq_i;
unsigned temp_t_seq_i = t_seq_i;
unsigned temp_h_node_index = h_node_index;
unsigned temp_t_node_index = t_node_index;

// change the last base
NTMC64_changelast(draft_char, index_char, opt::k, opt::h, temp_fhVal, temp_rhVal, hVal);
Expand Down Expand Up @@ -2520,15 +2514,14 @@ main(int argc, char** argv) // NOLINT
}

// VCF file reading RLW 19AUG2023
std::string line;
std::map<std::string, std::string> clinvar;

// check the vcf file is specified
if (!opt::vcf_filename.empty()) {
// if the file is specified check that it is readable
assert_readable(opt::vcf_filename);
// read file handle

std::string line;
// check if vcf is gzipped
if (opt::vcf_filename.substr(opt::vcf_filename.find_last_of(".") + 1) == "gz") {
std::ifstream myfile(opt::vcf_filename, std::ios_base::in | std::ios_base::binary);
Expand Down