diff --git a/argparse.cpp b/argparse.cpp index da7be76..90a0554 100644 --- 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 index 9dc907c..c6898b5 100644 --- 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 index fa2ba57..e50c4d7 100644 --- 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 index cb76951..2538bf7 100644 --- 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