Code reformating for clang complience

cpp/utils.cpp

 // utility functions for bioinformatics
-#include <iostream>
-#include <string>
+#include <algorithm>
+#include <cmath>
+#include <cstring>
 #include <fstream>
+#include <iostream>
 #include <sstream>
 #include <stdexcept>
-#include <cstring>
-#include <algorithm>
-#include <cmath>
+#include <string>
 #include <sys/time.h>
 #include <sys/types.h>
 
@@ -16,307 +16,257 @@
 #include "utils.h"
 using namespace std;
 using namespace boost::math;
+using boost::math::cdf;
 using boost::math::chi_squared;
-using boost::math::quantile;
 using boost::math::complement;
-using boost::math::cdf;
+using boost::math::quantile;
 
 // test if a file is readable
 // return value : true if readable ; false if not
-bool IsFileReadable( string file )
-{
-	ifstream fichier( file.c_str() );
-	return !fichier.fail();
+bool IsFileReadable(string file) {
+  ifstream fichier(file.c_str());
+  return !fichier.fail();
 }
 
 // display a time lenth in µs
 // return value : void
-void ExecMeasure( struct timeval begin , struct timeval end , string operation )
-{
-	cerr << "Execution time for operation : " << operation << " : "  << end.tv_usec - begin.tv_usec << " µs"  << endl;
+void ExecMeasure(struct timeval begin, struct timeval end, string operation) {
+  cerr << "Execution time for operation : " << operation << " : "
+       << end.tv_usec - begin.tv_usec << " µs" << endl;
 }
 
-
-int string_to_int( string incomingStr )
-{
-	istringstream isstmp( incomingStr );
-	int i;
-	isstmp >> i;
-	return i;
+int string_to_int(string incomingStr) {
+  istringstream isstmp(incomingStr);
+  int i;
+  isstmp >> i;
+  return i;
 }
 
-string double_to_string( double incoming )
-{
-	string result;
-	ostringstream oss;
-	oss << incoming;
-	result = oss.str();
-	return result;
+string double_to_string(double incoming) {
+  string result;
+  ostringstream oss;
+  oss << incoming;
+  result = oss.str();
+  return result;
 }
 
-
-string int_to_string( int incoming )
-{
-	string result;
-	ostringstream oss;
-	oss << incoming;
-	result = oss.str();
-	return result;
+string int_to_string(int incoming) {
+  string result;
+  ostringstream oss;
+  oss << incoming;
+  result = oss.str();
+  return result;
 }
 
-string pyReplace( string incoming , string pattern , string replacement )
-{
-	while (incoming.rfind( pattern ) != string::npos )
-	{
-		int n = incoming.rfind( pattern );
-		int l = pattern.length();
-
-		incoming.replace( n , l , replacement );
-	}
-	return incoming;
+string pyReplace(string incoming, string pattern, string replacement) {
+  while (incoming.rfind(pattern) != string::npos) {
+    int n = incoming.rfind(pattern);
+    int l = pattern.length();
+    incoming.replace(n, l, replacement);
+  }
+  return incoming;
 }
 
-string char_to_string(char incoming)
-{
-	string s;
-	stringstream ss;
-	ss << incoming;
-	ss >> s;
-	return s;
+string char_to_string(char incoming) {
+  string s;
+  stringstream ss;
+  ss << incoming;
+  ss >> s;
+  return s;
 }
 
-vector<string> parseOnSep( string inc , string sep )
-{
-	// cerr << "Entering ParseOnSep function" << endl;
-	// cerr << "\tIncoming string : " << inc << " ; separator : " << sep << endl;
-
-	vector<string> ret;
-	istringstream issInc (inc);
-	string mot;
-	while ( getline( issInc, mot, string_to_char( sep ) ) )
-	{
-		ret.push_back( mot );
-	}
-	return ret;
-
+vector<string> parseOnSep(string inc, string sep) {
+  // cerr << "Entering ParseOnSep function" << endl;
+  // cerr << "\tIncoming string : " << inc << " ; separator : " << sep << endl;
+
+  vector<string> ret;
+  istringstream issInc(inc);
+  string mot;
+  while (getline(issInc, mot, string_to_char(sep))) {
+    ret.push_back(mot);
+  }
+  return ret;
 }
 
-
-char string_to_char( string inc )
-{
-	char cstr[inc.size() + 1];
-	inc.copy(cstr, inc.size() + 1);
-	cstr[inc.size()] = '\0';
-	return *cstr;
+char string_to_char(string inc) {
+  char cstr[inc.size() + 1];
+  inc.copy(cstr, inc.size() + 1);
+  cstr[inc.size()] = '\0';
+  return *cstr;
 }
 
-
-
-
-string strip( string inc )
-{
-	cerr << "Passing into strip << " << inc ;
-	string::size_type pos = 0;
-	while ( ( pos = inc.find ("\n",pos) ) != string::npos )
-	{
-		cerr << " ; pos = " << pos ;
-		inc.erase ( pos, 2 );
-	}
-	cerr << " to " << inc << endl;
-	return inc;
+string strip(string inc) {
+  cerr << "Passing into strip << " << inc;
+  string::size_type pos = 0;
+  while ((pos = inc.find("\n", pos)) != string::npos) {
+    cerr << " ; pos = " << pos;
+    inc.erase(pos, 2);
+  }
+  cerr << " to " << inc << endl;
+  return inc;
 }
 
-double chisquare( vector<double> toTest , vector<double> all )
-{
-	boost::math::chi_squared chi(1);
-	double a1 = toTest[0] ;
-	double a2 = toTest[1];
-	double b1 = all[0];
-	double b2 = all[1];;
+double chisquare(vector<double> toTest, vector<double> all) {
+  boost::math::chi_squared chi(1);
+  double a1 = toTest[0];
+  double a2 = toTest[1];
+  double b1 = all[0];
+  double b2 = all[1];
+  ;
 
+  double s = a1 + a2 + b1 + b2;
+  double K = s * (a1 * b2 - a2 * b1) * (a1 * b2 - a2 * b1) / (a1 + a2) /
+             (b1 + b2) / (a1 + b1) / (a2 + b2);
+  double P = boost::math::cdf(chi, K);
 
-	double s = a1 + a2 + b1 + b2;
-	double K = s * (a1 * b2 - a2 * b1) * (a1 * b2 - a2 * b1) / (a1 + a2) / (b1 + b2) / (a1 + b1) / (a2 + b2);
-	double P = boost::math::cdf(chi, K);
-
-	return P;
+  return P;
 }
 
-
-double fisher_test(vector<double> toTest, vector<double> control )
-{
-	double a = toTest[0];
-	double b = toTest[1];
-	double c = control[0];
-	double d = control[1];
-
-	double N = a + b + c + d;
-	double r = a + c;
-	double n = c + d;
-	double max_for_k = min(r, n);
-	double min_for_k = (double)max(0, int(r + n - N));
-	hypergeometric_distribution<> hgd(r, n, N);
-	double cutoff = pdf(hgd, c);
-	double tmp_p = 0.0;
-	for(int k = min_for_k;k < max_for_k + 1;k++)
-	{
-		double p = pdf(hgd, k);
-		if(p <= cutoff)
-		{
-			tmp_p += p;
-		}
-	}
-	return tmp_p;
+double fisher_test(vector<double> toTest, vector<double> control) {
+  double a = toTest[0];
+  double b = toTest[1];
+  double c = control[0];
+  double d = control[1];
+
+  double N = a + b + c + d;
+  double r = a + c;
+  double n = c + d;
+  double max_for_k = min(r, n);
+  double min_for_k = (double)max(0, int(r + n - N));
+  hypergeometric_distribution<> hgd(r, n, N);
+  double cutoff = pdf(hgd, c);
+  double tmp_p = 0.0;
+  for (int k = min_for_k; k < max_for_k + 1; k++) {
+    double p = pdf(hgd, k);
+    if (p <= cutoff) {
+      tmp_p += p;
+    }
+  }
+  return tmp_p;
 }
 
-
-char checkBase(char incoming )
-{
-	if( incoming == 'c' )
-	{
-		return 'C';
-	}
-	if( incoming == 't' )
-	{
-		return 'T';
-	}
-	if( incoming == 'a' )
-	{
-		return 'A';
-	}
-	if( incoming == 'g' )
-	{
-		return 'G';
-	}
-	if( incoming == 'n' )
-	{
-		return 'N';
-	}
-	if( incoming == 'C' )
-	{
-		return 'C';
-	}
-	if( incoming == 'T' )
-	{
-		return 'T';
-	}
-	if( incoming == 'A' )
-	{
-		return 'A';
-	}
-	if( incoming == 'G' )
-	{
-		return 'G';
-	}
-	if( incoming == 'N' )
-	{
-		return 'N';
-	}
-	return 'N';
+char checkBase(char incoming) {
+  if (incoming == 'c') {
+    return 'C';
+  }
+  if (incoming == 't') {
+    return 'T';
+  }
+  if (incoming == 'a') {
+    return 'A';
+  }
+  if (incoming == 'g') {
+    return 'G';
+  }
+  if (incoming == 'n') {
+    return 'N';
+  }
+  if (incoming == 'C') {
+    return 'C';
+  }
+  if (incoming == 'T') {
+    return 'T';
+  }
+  if (incoming == 'A') {
+    return 'A';
+  }
+  if (incoming == 'G') {
+    return 'G';
+  }
+  if (incoming == 'N') {
+    return 'N';
+  }
+  return 'N';
 }
 
-
-
-//Method for calculating a sd from a vector of double
-double sd_calculator( vector<double> incVector )
-{
-	// Déclarations
-	double sd;
-	double temp_value;
-	double sumone = 0;
-	double sumtwo = 0;
-	double moyenne;
-	int number = 0;
-	double variance;
-
-	// calcul des moyennes et moyennes carrées
-	vector<double>::iterator myIter;
-	for( myIter = incVector.begin() ; myIter != incVector.end() ; myIter ++ )
-	{
-		temp_value = * myIter;
-
-		sumone += temp_value;
-		sumtwo += ( temp_value * temp_value );
-		number ++;
-	}
-
-	// calcul de la moyenne
-	moyenne = sumone / number;
-	// Calcul de la variance
-	variance = ( sumtwo / number ) - ( moyenne * moyenne );
-	// Calcul ecart type
-	sd = sqrt(variance);
-
-	return sd;
+// Method for calculating a sd from a vector of double
+double sd_calculator(vector<double> incVector) {
+  // Déclarations
+  double sd;
+  double temp_value;
+  double sumone = 0;
+  double sumtwo = 0;
+  double moyenne;
+  int number = 0;
+  double variance;
+
+  // calcul des moyennes et moyennes carrées
+  vector<double>::iterator myIter;
+  for (myIter = incVector.begin(); myIter != incVector.end(); myIter++) {
+    temp_value = *myIter;
+
+    sumone += temp_value;
+    sumtwo += (temp_value * temp_value);
+    number++;
+  }
+
+  // calcul de la moyenne
+  moyenne = sumone / number;
+  // Calcul de la variance
+  variance = (sumtwo / number) - (moyenne * moyenne);
+  // Calcul ecart type
+  sd = sqrt(variance);
+
+  return sd;
 }
 
 // Method for calculating a mean from a vector of double
-double moyenne_calculator( vector<double> incVector )
-{
-	// Déclarations
-	double temp_value;
-	double sumone;
-	double moyenne;
-	int number = 0;
-
-	// calcul des moyennes et moyennes carrées
-	vector<double>::iterator myIter;
-	for( myIter = incVector.begin() ; myIter != incVector.end() ; myIter ++ )
-	{
-		temp_value = * myIter;
-		sumone += temp_value;
-		number ++;
-	}
-
-	// calcul de la moyenne
-	if( number != 0 )
-	{
-		moyenne = sumone / number;
-	}
-	else
-	{
-		return 0;
-	}
-	return moyenne;
+double moyenne_calculator(vector<double> incVector) {
+  // Déclarations
+  double temp_value;
+  double sumone;
+  double moyenne;
+  int number = 0;
+
+  // calcul des moyennes et moyennes carrées
+  vector<double>::iterator myIter;
+  for (myIter = incVector.begin(); myIter != incVector.end(); myIter++) {
+    temp_value = *myIter;
+    sumone += temp_value;
+    number++;
+  }
+
+  // calcul de la moyenne
+  if (number != 0) {
+    moyenne = sumone / number;
+  } else {
+    return 0;
+  }
+  return moyenne;
 }
 
 // Method for calculating fisher exact test 2-sided, return the pvalue.
-double FET( int a , int b , int c , int d )
-{
-	int n = a + b + c + d;
-	double logpCutOff = logHypergeometricProb( a , b , c , d );
-	double pFraction = 0;
-	double logpValue = 0;
-
-	for( int x = 0 ; x <= n ; x ++ )
-	{
-		if( ( a + b - x >= 0 ) && ( a + c - x >= 0 ) && ( d - a + x >= 0 ) )
-		{
-			double l = logHypergeometricProb( x , a + b - x , a + c - x , d - a + x );
-			if( l <= logpCutOff )
-			{
-				pFraction += exp( l - logpCutOff );
-			}
-		}
-	}
-	logpValue = logpCutOff + log( pFraction );
-
-	return exp(logpValue);
+double FET(int a, int b, int c, int d) {
+  int n = a + b + c + d;
+  double logpCutOff = logHypergeometricProb(a, b, c, d);
+  double pFraction = 0;
+  double logpValue = 0;
+
+  for (int x = 0; x <= n; x++) {
+    if ((a + b - x >= 0) && (a + c - x >= 0) && (d - a + x >= 0)) {
+      double l = logHypergeometricProb(x, a + b - x, a + c - x, d - a + x);
+      if (l <= logpCutOff) {
+        pFraction += exp(l - logpCutOff);
+      }
+    }
+  }
+  logpValue = logpCutOff + log(pFraction);
+
+  return exp(logpValue);
 }
 
 // method for calculating the hypergeometrical log value  for the FET.
-double logHypergeometricProb( int a , int b , int c  , int d )
-{
-	return logFactoriel( a + b ) + logFactoriel( c + d ) + logFactoriel( a + c ) + logFactoriel( b + d )- logFactoriel( a ) - logFactoriel( b ) - logFactoriel( c ) - logFactoriel( d ) - logFactoriel( a + b + c + d );
+double logHypergeometricProb(int a, int b, int c, int d) {
+  return logFactoriel(a + b) + logFactoriel(c + d) + logFactoriel(a + c) +
+         logFactoriel(b + d) - logFactoriel(a) - logFactoriel(b) -
+         logFactoriel(c) - logFactoriel(d) - logFactoriel(a + b + c + d);
 }
 
 // Method for calculating a log factoriel
-double logFactoriel( int inc )
-{
-	double ret;
-	for( ret = 0 ; inc > 0 ; inc -- )
-	{
-		ret += log( (double)inc );
-	}
-	return ret;
+double logFactoriel(int inc) {
+  double ret;
+  for (ret = 0; inc > 0; inc--) {
+    ret += log((double)inc);
+  }
+  return ret;
 }