Merge branch 'master' of https://github.com/smithlabcode/smithlab_cpp

Author: guilhermesena1

sam_record.cpp

@@ -108,9 +108,10 @@ operator<<(std::ostream &the_stream, const sam_rec &r) {
 }
 
 sam_rec::sam_rec(const string &line) {
-
+  /*
   istringstream iss; // ADS: change to set the buffer from "line"
-  iss.rdbuf()->pubsetbuf(const_cast<char*>(line.c_str()), line.size());
+  iss.rdbuf()->pubsetbuf(const_cast<char*>(line.c_str()), line.size());*/
+  istringstream iss(line);
   uint32_t will_become_mapq = 0; // to not read mapq as character
                                  // since it's uint8_t
   if (!(iss >>

smithlab_os.cpp

@@ -390,7 +390,11 @@ read_fasta_file_short_names(const string &filename,
   string line;
   while (getline(in, line)) {
     if (line[0] == '>') {
-      names.push_back(string(begin(line) + 1,
+      const auto first_space = line.find_first_of(" \t", 1);
+      if (first_space == string::npos)
+        names.push_back(line.substr(1));
+      else
+        names.push_back(string(begin(line) + 1,
                              begin(line) + line.find_first_of(" \t", 1)));
       sequences.push_back(string());
     }