diff --git a/Configuration/limits.txt b/Configuration/limits.txt index 75a12a0..f9d257a 100644 --- a/Configuration/limits.txt +++ b/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 diff --git a/src/FalcoConfig.cpp b/src/FalcoConfig.cpp index 747bfd6..fed31e9 100644 --- a/src/FalcoConfig.cpp +++ b/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; diff --git a/src/FalcoConfig.hpp b/src/FalcoConfig.hpp index 34e6852..4ec3a24 100644 --- a/src/FalcoConfig.hpp +++ b/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************************ diff --git a/src/OptionParser.cpp b/src/OptionParser.cpp index c250a3d..ea7111c 100644 --- a/src/OptionParser.cpp +++ b/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 &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 &arguments, string config_filename) { // The "2" below corresponds to the "about" and "help" options assert(options.size() >= 2); diff --git a/src/OptionParser.hpp b/src/OptionParser.hpp index 9fbfb18..9ac0f14 100644 --- a/src/OptionParser.hpp +++ b/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 &arguments); - void parse(const int argc, const char **argv, + void parse(const int argc, char *argv[], std::vector &arguments, std::string config_filename); diff --git a/src/falco.cpp b/src/falco.cpp index 815f844..0fd5955 100644 --- a/src/falco.cpp +++ b/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 =