Just formatting

Author: andrewdavidsmith

bisulfite_utils.cpp

@@ -1,7 +1,7 @@
 /*
  *    Part of SMITHLAB software
  *
- *    Copyright (C) 2008 Cold Spring Harbor Laboratory, 
+ *    Copyright (C) 2008 Cold Spring Harbor Laboratory,
  *                       University of Southern California and
  *                       Andrew D. Smith
  *
@@ -29,22 +29,23 @@
 using std::string;
 
 void
-bisulfite_treatment(std::mt19937 &generator, string &seq, double bs_rate, double meth_rate) {
-  std::uniform_real_distribution<double> dist(0.0,1.0);
-  
+bisulfite_treatment(std::mt19937 &generator, string &seq,
+                    double bs_rate, double meth_rate) {
+
+  std::uniform_real_distribution<double> unif(0.0,1.0);
+
   const size_t seq_len = seq.length() - 1;
   for (size_t i = 0; i < seq_len; ++i)
     if (toupper(seq[i]) == 'C') {
       // CpG
       if (toupper(seq[i + 1]) == 'G' &&
-	  (dist(generator) > meth_rate || dist(generator)< bs_rate)) {
-	seq[i] = 'T';
+          (unif(generator) > meth_rate || unif(generator) < bs_rate)) {
+        seq[i] = 'T';
       }
       // Regular C
-      else if (dist(generator) < bs_rate)
-	seq[i] = 'T';
+      else if (unif(generator) < bs_rate)
+        seq[i] = 'T';
     }
-  if (toupper(seq[seq_len]) == 'C' && dist(generator) < bs_rate)
+  if (toupper(seq[seq_len]) == 'C' && unif(generator) < bs_rate)
     seq[seq_len] = 'T';
 }
-

bisulfite_utils.hpp

@@ -1,24 +1,19 @@
-/*
- *    Part of SMITHLAB software
+/* Part of Smith lab software
  *
- *    Copyright (C) 2008 Cold Spring Harbor Laboratory, 
- *                       University of Southern California and
- *                       Andrew D. Smith
+ * Copyright (C) 2020 University of Southern California and
+ *                    Andrew D. Smith
  *
- *    Authors: Andrew D. Smith
+ * Authors: Andrew D. Smith
  *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
  *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * General Public License for more details.
  */
 
 
@@ -29,7 +24,7 @@
 #include <random>
 
 void
-bisulfite_treatment(std::mt19937 &generator, std::string &seq, 
-		    double bs_rate = 1.0, double meth_rate = 0.0);
+bisulfite_treatment(std::mt19937 &generator, std::string &seq,
+                    double bs_rate = 1.0, double meth_rate = 0.0);
 
 #endif