Formatting scan alignments c++ code using clang-Google formatter

neusomatic/cpp/msa.cpp

@@ -1,47 +1,44 @@
-#include <iostream>
-#include <iostream>
-#include <fstream>
-
-#include <seqan/store.h>
 #include <seqan/realign.h>
+#include <seqan/store.h>
+
+#include <fstream>
+#include <iostream>
 
-#include <msa_options.h>
+#include "msa_options.h"
 
-void MSA(neusomatic::Options const& opt)
-{    
-    using namespace seqan;
-    CharString seqFileName = opt.input().c_str();
-    SeqFileIn seqFileIn(toCString(seqFileName));
-    StringSet<CharString> ids;
-    StringSet<Dna5String> seqs;
-    try
-    {
-        readRecords(ids, seqs, seqFileIn);
-    }
-    catch (Exception const & e)
-    {
-        std::cout << "ERROR: " << e.what() << std::endl;
-        return;
-    }
-    int n = length(ids);
-    Align<Dna5String> align;
-    resize(rows(align), n);
-    for (int i = 0; i < n; ++i){
-        assignSource(row(align, i), seqs[i]);
-    }
+void MSA(neusomatic::Options const& opt) {
+  using namespace seqan;
+  CharString seqFileName = opt.input().c_str();
+  SeqFileIn seqFileIn(toCString(seqFileName));
+  StringSet<CharString> ids;
+  StringSet<Dna5String> seqs;
+  try {
+    readRecords(ids, seqs, seqFileIn);
+  } catch (Exception const& e) {
+    std::cout << "ERROR: " << e.what() << std::endl;
+    return;
+  }
+  int n = length(ids);
+  Align<Dna5String> align;
+  resize(rows(align), n);
+  for (int i = 0; i < n; ++i) {
+    assignSource(row(align, i), seqs[i]);
+  }
 
-    globalMsaAlignment(align, SimpleScore(opt.match_score(), -opt.mismatch_score(), -opt.gap_extension_score(), -opt.gap_open_score()));
+  globalMsaAlignment(align,
+                     SimpleScore(opt.match_score(), -opt.mismatch_score(),
+                                 -opt.gap_extension_score(), -opt.gap_open_score()));
 
-    std::ofstream outfile;
-    outfile.open(opt.output().c_str());
-    for (int i = 0; i < n; ++i){
-	    outfile << ">" << ids[i] << "\n";
-	    outfile << row(align, i) << "\n";
-	}
-    outfile.close();
+  std::ofstream outfile;
+  outfile.open(opt.output().c_str());
+  for (int i = 0; i < n; ++i) {
+    outfile << ">" << ids[i] << "\n";
+    outfile << row(align, i) << "\n";
+  }
+  outfile.close();
 }
 
-int main(int argc, char *argv []) {
+int main(int argc, char* argv[]) {
   neusomatic::Options opt(argc, argv);
   MSA(opt);
   return 0;