Updating source files that use bamxx::bgzf_file

Author: andrewdavidsmith

src/analysis/hmr-rep.cpp

@@ -47,7 +47,7 @@ using std::to_string;
 using std::begin;
 using std::end;
 
-using bgzf_file = bamxx::bam_bgzf;
+using bamxx::bgzf_file;
 
 static GenomicRegion
 as_gen_rgn(const MSite &s) {

src/analysis/hmr.cpp

@@ -48,7 +48,7 @@ using std::runtime_error;
 using std::to_string;
 using std::unordered_set;
 
-using bgzf_file = bamxx::bam_bgzf;
+using bamxx::bgzf_file;
 
 static GenomicRegion
 as_gen_rgn(const MSite &s) {

src/analysis/hypermr.cpp

@@ -61,12 +61,12 @@ as_gen_rgn(const MSite &s) {
 static void
 load_cpgs(const string &cpgs_file, vector<MSite> &cpgs,
           vector<pair<double, double>> &meth) {
-  bamxx::bam_bgzf in(cpgs_file, "r");
+  bamxx::bgzf_file in(cpgs_file, "r");
   if (!in) throw runtime_error("failed opening file: " + cpgs_file);
 
   MSite the_site;
   string line;
-  while (in.getline(line)) cpgs.push_back(MSite(line));
+  while (getline(in, line)) cpgs.push_back(MSite(line));
 
   meth.resize(cpgs.size());
   for (size_t i = 0; i < cpgs.size(); ++i)

src/analysis/levels.cpp

@@ -52,7 +52,7 @@ using std::string;
 using std::to_string;
 using std::vector;
 
-using bgzf_file = bamxx::bam_bgzf;
+using bamxx::bgzf_file;
 
 enum class counts_file_format { ordinary, asym_cpg, sym_cpg };
 

src/analysis/methcounts.cpp

@@ -239,7 +239,7 @@ tag_with_mut(const uint32_t tag, const bool mut) {
 
 
 static void
-write_output(const bamxx::bam_header &hdr, bamxx::bam_bgzf &out,
+write_output(const bamxx::bam_header &hdr, bamxx::bgzf_file &out,
              const int32_t tid, const string &chrom,
              const vector<CountSet> &counts, bool CPG_ONLY) {
 
@@ -267,8 +267,7 @@ write_output(const bamxx::bam_header &hdr, bamxx::bam_bgzf &out,
           << tag_values[tag_with_mut(the_tag, mut)] << '\t'
           << (n_reads > 0 ? unconverted/n_reads : 0.0) << '\t'
           << n_reads << '\n';
-      const size_t expected_size = buf.tellp();
-      if (out.write(buf.c_str(), expected_size))
+      if (out.write(buf.c_str(), buf.tellp()))
         throw dnmt_error("error writing output");
     }
   }
@@ -397,7 +396,7 @@ process_reads(const bool VERBOSE,
 
   // open the output file
   const string output_mode = compress_output ? "w" : "wu";
-  bamxx::bam_bgzf out(outfile, output_mode);
+  bamxx::bgzf_file out(outfile, output_mode);
   if (!out) throw dnmt_error("error opening output file: " + outfile);
 
   /* set the threads for the input file decompression */

src/analysis/multimethstat.cpp

@@ -49,7 +49,7 @@ using std::ifstream;
 using std::isfinite;
 using std::is_sorted;
 
-using bgzf_file = bamxx::bam_bgzf;
+using bamxx::bgzf_file;
 
 static pair<bool, bool>
 meth_unmeth_calls(const size_t n_meth, const size_t n_unmeth) {
@@ -174,7 +174,7 @@ process_with_cpgs_loaded(const bool VERBOSE,
   if (!in) throw runtime_error("cannot open file: " + cpgs_file);
 
   string header;
-  in.getline(header);
+  getline(in, header);
 
   std::istringstream iss(header);
   string col_name;
@@ -197,7 +197,7 @@ process_with_cpgs_loaded(const bool VERBOSE,
   vector<vector<double> > values;
   MSite the_cpg;
   string line;
-  while (in.getline(line)) {
+  while (getline(in, line)) {
     values.push_back(vector<double>());
     get_site_and_values(line, the_cpg, values.back());
     cpgs.push_back(the_cpg);

src/analysis/pmd.cpp

@@ -52,7 +52,7 @@ using std::ostream;
 using std::ofstream;
 using std::to_string;
 
-using bgzf_file = bamxx::bam_bgzf;
+using bamxx::bgzf_file;
 
 static void
 get_adjacent_distances(const vector<GenomicRegion> &pmds,
@@ -739,7 +739,7 @@ check_if_array_data(const string &infile) {
   if (!in) throw std::runtime_error("bad file: " + infile);
 
   std::string line;
-  in.getline(line);
+  getline(in, line);
   std::istringstream iss(line);
   std::string chrom, pos, strand, seq, meth, cov;
   iss >> chrom >> pos >> strand >> seq >> meth;

src/analysis/roimethstat.cpp

@@ -51,7 +51,7 @@ using std::isfinite;
 using std::is_sorted;
 using std::regex_match;
 
-using bgzf_file = bamxx::bam_bgzf;
+using bamxx::bgzf_file;
 
 static pair<bool, bool>
 meth_unmeth_calls(const size_t n_meth, const size_t n_unmeth) {
@@ -480,7 +480,7 @@ Columns (beyond the first 6) in the BED format output:
       throw runtime_error("format must be 3 or 6+ column bed: " + regions_file);
     if (is_msite_file(regions_file)) {
       cerr << opt_parse.help_message() << endl;
-      throw runtime_error("The file seems to be a methylation file: " + 
+      throw runtime_error("The file seems to be a methylation file: " +
           regions_file + "\nCheck the order of the input arguments");
     }
     if (!is_msite_file(cpgs_file)) {
@@ -533,6 +533,3 @@ Columns (beyond the first 6) in the BED format output:
   }
   return EXIT_SUCCESS;
 }
-
-
-

src/common/MSite.hpp

@@ -140,19 +140,19 @@ find_offset_for_msite(const std::string &chrom,
 
 // ADS: using the functions below for now for static polymorphism
 // because I don't want to have insertion and extraction operators
-// hanging around for MSite with bamxx::bam_bgzf. The reason is that
+// hanging around for MSite with bamxx::bgzf_file. The reason is that
 // if we are going to use them, we need to be aware of which functions
 // we are calling, and not just do it unconsciously.
 
 #include <bamxx.hpp>
 #include <sstream>
 
-inline bamxx::bam_bgzf &
-write_site(bamxx::bam_bgzf &f, const MSite &s) {
+inline bamxx::bgzf_file &
+write_site(bamxx::bgzf_file &f, const MSite &s) {
   // ADS: to slow??
   std::ostringstream oss;
   oss << s.tostring() << '\n';
-  f.write(oss.str().c_str(), oss.str().size());
+  f.write(oss.str());
   return f;
 }
 
@@ -161,10 +161,10 @@ write_site(std::ostream &out, const MSite &s) {
   return out << s << '\n';
 }
 
-inline bamxx::bam_bgzf &
-read_site(bamxx::bam_bgzf &f, MSite &s) {
+inline bamxx::bgzf_file &
+read_site(bamxx::bgzf_file &f, MSite &s) {
   std::string line;
-  if (f.getline(line))
+  if (getline(f, line))
     s = MSite(line);
   return f;
 }

src/radmeth/methdiff.cpp

@@ -42,7 +42,7 @@ using std::vector;
 using std::ofstream;
 using std::ostream_iterator;
 
-using bgzf_file = bamxx::bam_bgzf;
+using bamxx::bgzf_file;
 
 static inline double
 log_sum_log(const double p, const double q) {
@@ -113,7 +113,7 @@ write_methdiff_site(bgzf_file &out, const MSite &a, const MSite &b,
       << b.n_meth() << '\t'
       << b.n_unmeth() << '\n';
   // clang-format on
-  out.write(oss.str().c_str(), oss.str().size());
+  out.write(oss.str());
   return out;
 }