most source files: updating the signature for argv to be non-const

Author: andrewdavidsmith

src/amrfinder/allelicmeth.cpp

@@ -213,7 +213,7 @@ verify_chroms_available(const string &chrom_name,
 
 
 int
-main_allelicmeth(int argc, const char **argv) {
+main_allelicmeth(int argc, char *argv[]) {
 
   try {
 

src/amrfinder/amrfinder.cpp

@@ -403,7 +403,7 @@ struct rename_amr {
 };
 
 int
-main_amrfinder(int argc, const char **argv) {
+main_amrfinder(int argc, char *argv[]) {
   try {
     const std::string description =
       "identify regions of allele-specific methylation";

src/amrfinder/amrtester.cpp

@@ -187,7 +187,7 @@ ensure_regions_are_named(vector<GenomicRegion> &regions) {
 
 
 int
-main_amrtester(int argc, const char **argv) {
+main_amrtester(int argc, char *argv[]) {
 
   try {
 

src/analysis/bsrate.cpp

@@ -468,7 +468,7 @@ write_per_read_histogram(const vector<vector<T>> &tab, const size_t n_hist_bins,
 }
 
 int
-main_bsrate(int argc, const char **argv) {
+main_bsrate(int argc, char *argv[]) {
   try {
     // assumed maximum length of a fragment
     static constexpr const size_t output_size = 10000;

src/analysis/cpgbins.cpp

@@ -195,7 +195,7 @@ process_chrom(const bool report_more_info, const string &chrom_name,
 }
 
 int
-main_cpgbins(int argc, const char **argv) {
+main_cpgbins(int argc, char *argv[]) {
   try {
     static const string description = R"""(
 Compute average site methylation levels in each non-overlapping

src/analysis/hmr-rep.cpp

@@ -338,7 +338,7 @@ split_comma(const string &orig) {
 }
 
 int
-main_hmr_rep(int argc, const char **argv) {
+main_hmr_rep(int argc, char *argv[]) {
 
   try {
 

src/analysis/hmr.cpp

@@ -386,7 +386,7 @@ check_sorted_within_chroms(T first, const T last) {
 }
 
 int
-main_hmr(int argc, const char **argv) {
+main_hmr(int argc, char *argv[]) {
 
   try {
 

src/analysis/hypermr.cpp

@@ -212,7 +212,7 @@ initialize_transitions(vector<vector<double>> &trans) {
 }
 
 int
-main_hypermr(int argc, const char **argv) {
+main_hypermr(int argc, char *argv[]) {
   try {
     static const string description =
       "Identify regions of elevated methylation. Designed for "

src/analysis/levels.cpp

@@ -83,7 +83,7 @@ guess_counts_file_format(const string &filename) {
 }
 
 int
-main_levels(int argc, const char **argv) {
+main_levels(int argc, char *argv[]) {
   try {
     bool verbose = false;
     bool relaxed_mode = false;

src/analysis/metagene.cpp

@@ -86,7 +86,7 @@ collapse_bins(const uint32_t bin_size, vector<T> &v) {
 }
 
 int
-metagene(int argc, const char **argv) {
+metagene(int argc, char *argv[]) {
   constexpr auto description =
     "Compute the information needed for metagene plots of DNA methylation    \
      levels. The columns in the output correspond to the fields calculated   \