From 2e466787775ded77b65408bdeba2e8ea22320bd7 Mon Sep 17 00:00:00 2001
From: Niema Moshiri <niemamoshiri@gmail.com>
Date: Tue, 5 Mar 2024 20:57:11 -0800
Subject: [PATCH] Updated variable types for stability

---
 argparse.h |  2 +-
 count.cpp  | 10 +++++-----
 primer.cpp |  4 ++--
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/argparse.h b/argparse.h
index ca04d18..9dc907c 100644
--- a/argparse.h
+++ b/argparse.h
@@ -12,7 +12,7 @@ struct args_t {
     //int16_t num_threads = DEFAULT_NUM_THREADS;   // number of threads
     uint8_t min_qual = DEFAULT_MIN_QUAL;           // minimum base quality to count base in counts
     COUNT_T min_depth = DEFAULT_MIN_DEPTH;         // minimum depth to call base in consensus
-    double min_freq = DEFAULT_MIN_FREQ;            // minimum frequency to call base in consensus
+    long double min_freq = DEFAULT_MIN_FREQ;       // minimum frequency to call base in consensus
     char ambig = DEFAULT_AMBIG;                    // ambiguous symbol
     char* primer_bed_fn = nullptr;                 // primer bed filename
     int16_t primer_offset = DEFAULT_PRIMER_OFFSET; // number of bases after primer to also trim
diff --git a/count.cpp b/count.cpp
index 0522ccc..f17f40c 100644
--- a/count.cpp
+++ b/count.cpp
@@ -2,8 +2,8 @@
 
 void write_pos_counts_tsv(std::vector<std::array<COUNT_T, 5>> const & pos_counts, std::ostream & out_file, char delim) {
     out_file << "Pos" << delim << 'A' << delim << 'C' << delim << 'G' << delim << 'T' << delim << '-' << delim << "Total" << std::endl;
-    long unsigned int const pos_counts_size = pos_counts.size(); COUNT_T row_sum;
-    for(long unsigned int pos = 0; pos < pos_counts_size; ++pos) {
+    uint64_t const pos_counts_size = pos_counts.size(); COUNT_T row_sum;
+    for(uint64_t pos = 0; pos < pos_counts_size; ++pos) {
         out_file << pos; row_sum = 0;
         for(auto & val : pos_counts[pos]) {
             out_file << delim << val; row_sum += val;
@@ -225,10 +225,10 @@ counts_t compute_counts(const char* const in_reads_fn, std::string const & ref,
 
 std::string compute_consensus(std::vector<std::array<COUNT_T, 5>> const & pos_counts, std::unordered_map<uint32_t, std::unordered_map<std::string, COUNT_T>> & ins_counts, args_t const & user_args) {
     std::string out; out.reserve(FASTA_STRING_RESERVE);
-    long unsigned int const pos_counts_size = pos_counts.size();
+    uint64_t const pos_counts_size = pos_counts.size();
     std::unordered_map<uint32_t, std::unordered_map<std::string, COUNT_T>>::iterator ins_counts_it;
-    char best_pos_base; std::string best_ins_seq = ""; long unsigned int best_count; long unsigned int tot_depth;
-    for(long unsigned int pos = 0; pos <= pos_counts_size; ++pos) {
+    char best_pos_base; std::string best_ins_seq = ""; uint64_t best_count; uint64_t tot_depth;
+    for(uint64_t pos = 0; pos <= pos_counts_size; ++pos) {
         // handle insertions before pos
         ins_counts_it = ins_counts.find(pos);
         if(ins_counts_it != ins_counts.end()) {
diff --git a/primer.cpp b/primer.cpp
index 85553cd..413916c 100644
--- a/primer.cpp
+++ b/primer.cpp
@@ -34,9 +34,9 @@ std::vector<std::pair<uint32_t, uint32_t>> find_overlapping_primers(uint32_t con
     }
     min_max_primer_inds.resize(ref_len, std::make_pair((uint32_t)-1,(uint32_t)-1));
     std::vector<std::pair<uint32_t, uint32_t>> primers = read_bed(primer_bed_fn);
-    unsigned long const NUM_PRIMERS = primers.size();
+    uint64_t const NUM_PRIMERS = primers.size();
     std::list<const std::pair<uint32_t, uint32_t>*> curr_primers;
-    unsigned long primers_ind = 0;
+    uint64_t primers_ind = 0;
     for(uint32_t pos = 0; pos < ref_len; ++pos) {
         while(!curr_primers.empty() && pos >= curr_primers.front()->second + primer_offset) {
             curr_primers.pop_front();