Merge pull request #233 from smithlabcode/bamxx-submodule-update

Updating bamxx submodule

src/analysis/cpgbins.cpp

@@ -75,25 +75,6 @@ format_levels_counter(const LevelsCounter &lc) {
   return oss.str();
 }
 
-inline auto
-getline(bgzf_file &file, kstring_t &line) -> bgzf_file & {
-  if (file.f == nullptr) return file;
-  const int x = bgzf_getline(file.f, '\n', &line);
-  if (x == -1) {
-    file.destroy();
-    free(line.s);
-    line = {0, 0, nullptr};
-  }
-  if (x < -1) {
-    // ADS: this is an error condition and should be handled
-    // differently from the EOF above.
-    file.destroy();
-    free(line.s);
-    line = {0, 0, nullptr};
-    throw runtime_error{"failed reading bgzf file"};
-  }
-  return file;
-}
 
 static unordered_map<string, uint64_t>
 get_chrom_sizes(const string &chrom_sizes_file) {
@@ -163,7 +144,7 @@ read_xsym_by_chrom(const uint32_t n_threads, const string &xsym_file) {
 
   vector<xsym_entry> curr_chrom;
 
-  while (getline(in, line)) {
+  while (bamxx::getline(in, line)) {
     if (is_counts_header_line(line.s)) continue;  // ADS: early loop exit
 
     if (!std::isdigit(line.s[0])) {  // check if we have a chrom line

src/common/counts_header.cpp

@@ -69,26 +69,6 @@ write_counts_header_from_file(const string &header_file, bgzf_file &out) {
 }
 
 
-inline bgzf_file &
-getline(bgzf_file &file, kstring_t &line) {
-  if (file.f == nullptr) return file;
-  const int x = bgzf_getline(file.f, '\n', &line);
-  if (x == -1) {
-    file.destroy();
-    free(line.s);
-    line = {0, 0, nullptr};
-  }
-  if (x < -1) {
-    // ADS: this is an error condition and should be handled
-    // differently from the EOF above.
-    file.destroy();
-    free(line.s);
-    line = {0, 0, nullptr};
-  }
-  return file;
-}
-
-
 bamxx::bgzf_file &
 skip_counts_header(bamxx::bgzf_file &in) {
 
@@ -97,7 +77,7 @@ skip_counts_header(bamxx::bgzf_file &in) {
   const int ret = ks_resize(&line, 1024);
   if (ret) return in;
 
-  while (getline(in, line) && line.s[0] == '#') {
+  while (bamxx::getline(in, line) && line.s[0] == '#') {
     if (line.s[0] == '#' && line.l == 1)
       return in;
   }

src/utils/covered.cpp

@@ -35,24 +35,6 @@ using std::string;
 
 using bamxx::bgzf_file;
 
-inline auto
-getline(bgzf_file &file, kstring_t &line) -> bgzf_file & {
-  if (file.f == nullptr) return file;
-  const int x = bgzf_getline(file.f, '\n', &line);
-  if (x == -1) {
-    file.destroy();
-    free(line.s);
-    line = {0, 0, nullptr};
-  }
-  if (x < -1) {
-    // ADS: this is an error condition and should be handled
-    // differently from the EOF above.
-    file.destroy();
-    free(line.s);
-    line = {0, 0, nullptr};
-  }
-  return file;
-}
 
 static inline bool
 get_is_mutated(const kstring_t &line) {
@@ -131,7 +113,7 @@ main_covered(int argc, const char **argv) {
     if (ret) throw runtime_error("failed to acquire buffer");
 
     bool write_ok = true;
-    while (getline(in, line) && write_ok) {
+    while (bamxx::getline(in, line) && write_ok) {
       const bool is_mutated = get_is_mutated(line);
       const uint32_t n_reads = get_n_reads(line);
       if (n_reads > 0u || is_mutated) {

src/utils/unxcounts.cpp

@@ -69,25 +69,6 @@ read_fasta_file_short_names_uppercase(const string &chroms_file,
               [](const char c) { return std::toupper(c); });
 }
 
-inline auto
-getline(bgzf_file &file, kstring_t &line) -> bgzf_file & {
-  if (file.f == nullptr) return file;
-  const int x = bgzf_getline(file.f, '\n', &line);
-  if (x == -1) {
-    file.destroy();
-    free(line.s);
-    line = {0, 0, nullptr};
-  }
-  if (x < -1) {
-    // ADS: this is an error condition and should be handled
-    // differently from the EOF above.
-    file.destroy();
-    free(line.s);
-    line = {0, 0, nullptr};
-    throw runtime_error{"failed reading bgzf file"};
-  }
-  return file;
-}
 
 static void
 verify_chrom_orders(const bool verbose, const uint32_t n_threads,
@@ -108,7 +89,7 @@ verify_chrom_orders(const bool verbose, const uint32_t n_threads,
   const int ret = ks_resize(&line, 1024);
   if (ret) throw runtime_error("failed to acquire buffer");
 
-  while (getline(in, line)) {
+  while (bamxx::getline(in, line)) {
     if (std::isdigit(line.s[0])) continue;
     if (is_counts_header_line(line.s)) continue;
 

src/utils/xcounts.cpp

@@ -45,25 +45,6 @@ using std::to_string;
 
 using bamxx::bgzf_file;
 
-inline auto
-getline(bgzf_file &file, kstring_t &line) -> bgzf_file & {
-  if (file.f == nullptr) return file;
-  const int x = bgzf_getline(file.f, '\n', &line);
-  if (x == -1) {
-    file.destroy();
-    free(line.s);
-    line = {0, 0, nullptr};
-  }
-  if (x < -1) {
-    // ADS: this is an error condition and should be handled
-    // differently from the EOF above.
-    file.destroy();
-    free(line.s);
-    line = {0, 0, nullptr};
-  }
-  return file;
-}
-
 
 template<typename T>
 static inline uint32_t
@@ -171,7 +152,7 @@ main_xcounts(int argc, const char **argv) {
     bool found_header = (!genome_file.empty() || !header_file.empty());
 
     MSite site;
-    while (status_ok && getline(in, line)) {
+    while (status_ok && bamxx::getline(in, line)) {
       if (is_counts_header_line(line.s)) {
         if (!genome_file.empty() || !header_file.empty()) continue;
         found_header = true;