Fixing indentation

Author: andrewdavidsmith

QualityScore.cpp

@@ -26,6 +26,7 @@
 #include "smithlab_utils.hpp"
 
 using std::string;
+using std::runtime_error;
 
 static bool
 check_formats(char c, bool &solexa, bool &phred) {
@@ -39,8 +40,8 @@ fastq_score_type(const string filename) {
   static const size_t MAX_LINE_SIZE = 1000;
   std::ifstream f(filename.c_str());
   if (!f)
-    throw SMITHLABException("cannot open input file " + string(filename));
-  
+    throw runtime_error("cannot open input file " + filename);
+
   char line[MAX_LINE_SIZE];
   bool solexa = true, phred = true;
   size_t line_count = 0;
@@ -49,7 +50,7 @@ fastq_score_type(const string filename) {
       char *c = line;
       while (*c != '\0' && check_formats(*c, solexa, phred)) ++c;
       if (!check_formats(*c, solexa, phred))
-	return ((phred) ? FASTQ_Phred : FASTQ_Solexa);
+        return ((phred) ? FASTQ_Phred : FASTQ_Solexa);
     }
     ++line_count;
   }
@@ -61,25 +62,25 @@ mapped_reads_score_type(const string filename) {
   static const size_t MAX_LINE_SIZE = 10000;
   std::ifstream f(filename.c_str());
   if (!f)
-    throw SMITHLABException("cannot open input file " + string(filename));
-  
+    throw runtime_error("cannot open input file " + filename);
+
   char line[MAX_LINE_SIZE];
   bool solexa = true, phred = true;
   while (f.getline(line, MAX_LINE_SIZE)) {
     size_t space_count = 0, position = 0;
     while (space_count < 7) {
       while (position < MAX_LINE_SIZE && isspace(line[position]))
-	++position;
+        ++position;
       if (position == MAX_LINE_SIZE)
-	throw SMITHLABException("line too long in file: " + filename);
+        throw runtime_error("line too long in file: " + filename);
       while (position < MAX_LINE_SIZE && !isspace(line[position]))
-	++position;
+        ++position;
       if (position == MAX_LINE_SIZE)
-	throw SMITHLABException("line too long in file: " + filename);
+        throw runtime_error("line too long in file: " + filename);
       ++space_count;
     }
     if (space_count < 7)
-      throw SMITHLABException("malformed line in file: " + filename);
+      throw runtime_error("malformed line in file: " + filename);
     while (position < MAX_LINE_SIZE && isspace(line[position]))
       ++position;
     char *c = line + position;