Fix formatting in source files.

Author: Parsoa

bed_utils.hpp

@@ -3,14 +3,14 @@
 
 #include <vector>
 #include <string>
-#include <unordered_map>
+#include <fstream>
 #include <sstream>
 #include <iostream>
 #include <iterator>
-#include <algorithm>
-#include <fstream>
 #include <stdlib.h>
 #include <assert.h>
+#include <algorithm>
+#include <unordered_map>
 
 #include "lprint.hpp"
 

converter.cpp

@@ -3,49 +3,49 @@
 KSEQ_INIT(gzFile, gzread)
 
 void Converter::run() {
-  auto c = Configuration::getInstance();
-  string fq_path = c->fastq;
-  string sfs_path = c->bed;
-  int tau = c->cutoff;
+    auto c = Configuration::getInstance();
+    string fq_path = c->fastq;
+    string sfs_path = c->bed;
+    int tau = c->cutoff;
 
-  // 1 Parsing and storing sfss
-  map<string, vector<SFS>> SFSs = parse_sfsfile(sfs_path, tau);
+    // 1 Parsing and storing sfss
+    map<string, vector<SFS>> SFSs = parse_sfsfile(sfs_path, tau);
 
-  // 2 Parsing reads
-  map<string, uint> allsfs;
-  gzFile fp = gzopen(fq_path.c_str(), "r");
-  kseq_t *seq = kseq_init(fp);
-  int l;
-  uint idx = 0;
-  while ((l = kseq_read(seq)) >= 0) {
-    string header = seq->name.s;
-    if (SFSs.find(header) == SFSs.end()) {
-      // cerr << "Skipping " << header << endl;
-      continue;
-    }
-    for (const SFS &sfs : SFSs.at(header)) {
-      uint st = sfs.s;
-      uint len = sfs.l;
-      uint c = sfs.c;
-      string sfsseq(seq->seq.s, st, len);
-
-      string rcsfsseq(sfsseq);
-      for (uint j = 0; j < sfsseq.size(); ++j)
-        rcsfsseq[j] = RCN[sfsseq[j]];
-      reverse(rcsfsseq.begin(), rcsfsseq.end());
-      sfsseq = min(sfsseq, rcsfsseq);
+    // 2 Parsing reads
+    map<string, uint> allsfs;
+    gzFile fp = gzopen(fq_path.c_str(), "r");
+    kseq_t *seq = kseq_init(fp);
+    int l;
+    uint idx = 0;
+    while ((l = kseq_read(seq)) >= 0) {
+        string header = seq->name.s;
+        if (SFSs.find(header) == SFSs.end()) {
+        // cerr << "Skipping " << header << endl;
+            continue;
+        }
+        for (const SFS &sfs : SFSs.at(header)) {
+            uint st = sfs.s;
+            uint len = sfs.l;
+            uint c = sfs.c;
+            string sfsseq(seq->seq.s, st, len);
+            string rcsfsseq(sfsseq);
+            for (uint j = 0; j < sfsseq.size(); ++j) {
+                rcsfsseq[j] = RCN[sfsseq[j]];
+            }
+            reverse(rcsfsseq.begin(), rcsfsseq.end());
+            sfsseq = min(sfsseq, rcsfsseq);
 
-      string qual(len, '-');
-      cout << "@" << header << "#" << idx << "#" << st << "#" << st + len - 1
-           << "#" << c << "\n"
-           << sfsseq << "\n"
-           << "+"
-           << "\n"
-           << qual << endl;
-      ++idx;
+            string qual(len, '-');
+            cout << "@" << header << "#" << idx << "#" << st << "#" << st + len - 1
+                << "#" << c << "\n"
+                << sfsseq << "\n"
+                << "+"
+                << "\n"
+                << qual << endl;
+            ++idx ;
+        }
     }
-  }
 
-  kseq_destroy(seq);
-  gzclose(fp);
+    kseq_destroy(seq);
+    gzclose(fp);
 }

converter.hpp

@@ -1,17 +1,19 @@
 #ifndef CONVERTER_HPP
 #define CONVERTER_HPP
 
-#include "config.hpp"
-#include "kseq.h"
-#include "sfsutils.hpp"
 #include <algorithm>
+
+#include "kseq.h"
 #include <zlib.h>
 
+#include "config.hpp"
+#include "sfsutils.hpp"
+
 using namespace std;
 
 class Converter {
 public:
-  void run();
+    void run();
 };
 
 #endif