Fixing newlines for sensible parsing

Configuration/limits.txt

@@ -1,81 +1,81 @@
-# For each of the modules you can choose to not run that
-# module at all by setting the value below to 1 for the
-# modules you want to remove.
-duplication 		ignore 		0
-kmer 				ignore 		1
-n_content 			ignore 		0
-overrepresented 	ignore 		0
-quality_base 		ignore 		0
-sequence 			ignore 		0
-gc_sequence			ignore 		0
-quality_sequence	ignore		0
-tile				ignore		0
-sequence_length		ignore		0
-adapter				ignore		0
-
-# For the duplication module the value is the percentage
-# remaining after deduplication.  Measured levels below
-# these limits trigger the warning / error.
-duplication	warn	70
-duplication error	50
-
-# For the kmer module the filter is on the -log10 binomial
-# pvalue for the most significant Kmer, so 5 would be 
-# 10^-5 = p<0.00001
-kmer	warn	2
-kmer	error	5
-
-# For the N module the filter is on the percentage of Ns
-# at any position in the library
-n_content	warn	5
-n_content	error	20
-
-# For the overrepresented seqs the warn value sets the
-# threshold for the overrepresented sequences to be reported
-# at all as the proportion of the library which must be seen
-# as a single sequence
-overrepresented	warn	0.1
-overrepresented	error	1
-
-# The per base quality filter uses two values, one for the value
-# of the lower quartile, and the other for the value of the
-# median quality.  Failing either of these will trigger the alert
-quality_base_lower	warn	10
-quality_base_lower	error	5
-quality_base_median	warn	25
-quality_base_median	error	20
-
-# The per base sequence content module tests the maximum deviation
-# between A and T or C and G
-sequence	warn	10
-sequence	error	20
-
-# The per sequence GC content tests the maximum deviation between
-# the theoretical distribution and the real distribution
-gc_sequence	warn	15
-gc_sequence	error	30
-
-# The per sequence quality module tests the phred score which is
-# most frequently observed
-quality_sequence	warn	27
-quality_sequence	error	20
-
-# The per tile module tests the maximum phred score loss between 
-# and individual tile and the average for that base across all tiles
-tile	warn	5
-tile	error	10
-
-# The sequence length module tests are binary, so the values here
-# simply turn them on or off.  The actual tests warn if you have
-# sequences of different length, and error if you have sequences
-# of zero length.
-
-sequence_length	warn	1
-sequence_length	error	1
-
-# The adapter module's warnings and errors are based on the 
-# percentage of reads in the library which have been observed
-# to contain an adapter associated Kmer at any point
-
-adapter	warn 5
-adapter	error	10
+# For each of the modules you can choose to not run that
+# module at all by setting the value below to 1 for the
+# modules you want to remove.
+duplication 		ignore 		0
+kmer 				ignore 		1
+n_content 			ignore 		0
+overrepresented 	ignore 		0
+quality_base 		ignore 		0
+sequence 			ignore 		0
+gc_sequence			ignore 		0
+quality_sequence	ignore		0
+tile				ignore		0
+sequence_length		ignore		0
+adapter				ignore		0
+
+# For the duplication module the value is the percentage
+# remaining after deduplication.  Measured levels below
+# these limits trigger the warning / error.
+duplication	warn	70
+duplication error	50
+
+# For the kmer module the filter is on the -log10 binomial
+# pvalue for the most significant Kmer, so 5 would be
+# 10^-5 = p<0.00001
+kmer	warn	2
+kmer	error	5
+
+# For the N module the filter is on the percentage of Ns
+# at any position in the library
+n_content	warn	5
+n_content	error	20
+
+# For the overrepresented seqs the warn value sets the
+# threshold for the overrepresented sequences to be reported
+# at all as the proportion of the library which must be seen
+# as a single sequence
+overrepresented	warn	0.1
+overrepresented	error	1
+
+# The per base quality filter uses two values, one for the value
+# of the lower quartile, and the other for the value of the
+# median quality.  Failing either of these will trigger the alert
+quality_base_lower	warn	10
+quality_base_lower	error	5
+quality_base_median	warn	25
+quality_base_median	error	20
+
+# The per base sequence content module tests the maximum deviation
+# between A and T or C and G
+sequence	warn	10
+sequence	error	20
+
+# The per sequence GC content tests the maximum deviation between
+# the theoretical distribution and the real distribution
+gc_sequence	warn	15
+gc_sequence	error	30
+
+# The per sequence quality module tests the phred score which is
+# most frequently observed
+quality_sequence	warn	27
+quality_sequence	error	20
+
+# The per tile module tests the maximum phred score loss between
+# and individual tile and the average for that base across all tiles
+tile	warn	5
+tile	error	10
+
+# The sequence length module tests are binary, so the values here
+# simply turn them on or off.  The actual tests warn if you have
+# sequences of different length, and error if you have sequences
+# of zero length.
+
+sequence_length	warn	1
+sequence_length	error	1
+
+# The adapter module's warnings and errors are based on the
+# percentage of reads in the library which have been observed
+# to contain an adapter associated Kmer at any point
+
+adapter	warn 5
+adapter	error	10

src/FalcoConfig.cpp

@@ -308,7 +308,7 @@ strip_path(string full_path) {
 /******************** FALCOCONFIG FUNCTIONS *************************/
 /********************************************************************/
 // Default config properties
-FalcoConfig::FalcoConfig(const int argc, const char **argv) {
+FalcoConfig::FalcoConfig(const int argc, char *argv[]) {
   casava = false;
   nanopore = false;
   nofilter = false;

src/FalcoConfig.hpp

@@ -31,7 +31,7 @@
 // config from options, constants, magic numbers, etc
 struct FalcoConfig {
   static const std::string FalcoVersion;
-  FalcoConfig(const int argc, const char **argv);
+  FalcoConfig(const int argc, char *argv[]);
 
   /************************************************************
    *************** FASTQC OPTION PARSER************************

src/OptionParser.cpp

@@ -410,7 +410,7 @@ read_config_file(const string &config_filename,
 }
 
 void
-OptionParser::parse(const int argc, const char **argv,
+OptionParser::parse(const int argc, char *argv[],
                     vector<string> &arguments) {
   // The "2" below corresponds to the "about" and "help" options
   assert(options.size() >=  2);
@@ -454,7 +454,7 @@ OptionParser::parse(const int argc, const char **argv,
 }
 
 void
-OptionParser::parse(const int argc, const char **argv,
+OptionParser::parse(const int argc, char *argv[],
                     vector<string> &arguments, string config_filename) {
   // The "2" below corresponds to the "about" and "help" options
   assert(options.size() >=  2);

src/OptionParser.hpp

@@ -107,10 +107,10 @@ class OptionParser {
   void add_opt(const std::string l_name, const char s_name,
                const std::string descr,  const bool reqd, char &val);
 
-  void parse(const int argc, const char **argv,
+  void parse(const int argc, char *argv[],
              std::vector<std::string> &arguments);
 
-  void parse(const int argc, const char **argv,
+  void parse(const int argc, char *argv[],
              std::vector<std::string> &arguments,
              std::string config_filename);
 

src/falco.cpp

@@ -267,7 +267,7 @@ file_exists(const std::string &file_name) {
 }
 
 int
-main(int argc, const char **argv) {
+main(int argc, char *argv[]) {
 
   try {
     static const std::string FALCO_VERSION =