More variable type updates

niemasd · Mar 6, 2024 · 91703e5 · 91703e5
1 parent 2e46678
commit 91703e5
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Showing 4 changed files with 1 addition and 4 deletions.
diff --git a/argparse.cpp b/argparse.cpp
@@ -145,7 +145,6 @@ void print_usage(const char* const exe_name="viral_consensus_mp", std::ostream &
         << "  -o/--out_consensus OUT_CONSENSUS      Output consensus genome (FASTA), or '-' for standard output" << std::endl
         << "  -op/--out_pos_counts OUT_POS_COUNTS   Output position counts (TSV), or '-' for standard output (default: don't output)" << std::endl
         << "  -oi/--out_ins_counts OUT_INS_COUNTS   Output insertion counts (JSON), or '-' for standard output (default: don't output)" << std::endl
-        //<< "  -t/--threads THREADS                  Number of threads (default: " << DEFAULT_NUM_THREADS << ")" << std::endl
         << "  -q/--min_qual MIN_QUAL                Minimum base quality to count base in counts (default: " << DEFAULT_MIN_QUAL << ")" << std::endl
         << "  -d/--min_depth MIN_DEPTH              Minimum depth to call base/insertion in consensus (default: " << DEFAULT_MIN_DEPTH << ")" << std::endl
         << "  -f/--min_freq MIN_FREQ                Minimum frequency to call base/insertion in consensus (default: " << DEFAULT_MIN_FREQ << ")" << std::endl

diff --git a/argparse.h b/argparse.h
@@ -9,7 +9,6 @@ struct args_t {
     char* out_consensus_fn = nullptr;              // output consensus genome filename (FASTA)
     char* out_pos_counts_fn = nullptr;             // output position counts filename (TSV)
     char* out_ins_counts_fn = nullptr;             // output insertion counts filename (JSON)
-    //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
     long double min_freq = DEFAULT_MIN_FREQ;       // minimum frequency to call base in consensus

diff --git a/common.cpp b/common.cpp
@@ -3,6 +3,6 @@
 void rev_comp_inplace(std::string & s) {
     std::string tmp = s; size_t l = s.length();
     for(size_t i = 0; i < l; ++i) {
-        s[i] = COMPLEMENT[(int)tmp[l-i-1]];
+        s[i] = COMPLEMENT[(uint8_t)tmp[l-i-1]];
     }
 }
diff --git a/common.h b/common.h
@@ -16,7 +16,6 @@
 #define VERSION "0.0.5"
 
 // definitions/constants for argparsing
-#define DEFAULT_NUM_THREADS 1
 #define DEFAULT_MIN_QUAL 20
 #define DEFAULT_MIN_DEPTH 10
 #define DEFAULT_MIN_FREQ 0.5