7 #ifndef FILTER_STEP_HPP_ 8 #define FILTER_STEP_HPP_ 12 #include "boost/property_tree/ptree_fwd.hpp" 28 "discard reads that have nucleotides other than specified" 41 std::vector<char>
ch_;
54 "discard reads with length outside of [min, max] rage" 82 "discard reads that contain a homopolymer longer than minimal length" 109 "discard reads that contain a quality score lower than minimal"
135 "discard reads with average quality score lower than minimal" 161 "find longest interval with each quality score greater than " 162 "minimal; discard reads where the interval found is shorter " 190 "find longest interval with average quality score greater than " 191 "minimal; discard reads where the interval found is shorter " 225 "Truncate reads to bring number of ambiguous bases below maximum" 229 "Find read interval at least min_len nucleotides long that has " 230 "at most max_ambiguous ambiguous nucleotides. " 231 "Discard reads where such interval cannot be found. " 232 "If min_len is zero, require that the whole read contains at most " 233 "max_ambiguous ambiguous nucleotides." VDJ_PIPE_STATIC_STRING_METHOD(comment,"discard reads that have nucleotides other than specified") Character_filter(Vm_access_single const &vma
void finish()
Definition: filter_step.hpp:38
Definition: filter_step.hpp:217
Definition: sanitize_string.cpp:15
Definition: filter_base.hpp:17
std::size_t min_len_
Definition: filter_step.hpp:212
std::size_t min_qual_l_
Definition: filter_step.hpp:209
void finish()
Definition: filter_step.hpp:145
std::size_t win_len_
Definition: filter_step.hpp:206
double min_
Definition: filter_step.hpp:148
value_type min_
Definition: filter_step.hpp:122
Definition: filter_step.hpp:127
Definition: value_map_access_single.hpp:16
Definition: filter_step.hpp:182
unsigned min_
Definition: filter_step.hpp:95
Qual_record::quality::value_type min_qual_
Definition: filter_step.hpp:176
Qual_record::quality::value_type value_type
Definition: filter_step.hpp:101
void finish()
Definition: filter_step.hpp:92
Definition: filter_base.hpp:51
void finish()
Definition: filter_step.hpp:202
Definition: filter_step.hpp:100
std::vector< char > ch_
Definition: filter_step.hpp:41
void finish()
Definition: filter_step.hpp:64
Main namespace of vdj_pipe library.
Definition: keywords_variable.hpp:11
Definition: filter_step.hpp:20
Definition: filter_step.hpp:153
std::size_t min_len_
Definition: filter_step.hpp:246
Definition: pipe_environment.hpp:26
Definition: filter_step.hpp:74
unsigned char value_type
Definition: sequence_record.hpp:37
boost::property_tree::ptree const & pt
Definition: filter_step.hpp:33
void finish()
Definition: filter_step.hpp:173
Definition: filter_step.hpp:46
std::size_t max_ambiguous_
Definition: filter_step.hpp:247
unsigned max_
Definition: filter_step.hpp:68
unsigned min_
Definition: filter_step.hpp:67
bool trim_
Definition: filter_step.hpp:69
void run()
Definition: filter_step.cpp:71
bpt::ptree ptree
Definition: processing_step_utils.hpp:19
std::size_t min_len_
Definition: filter_step.hpp:177
boost::property_tree::ptree const Pipe_environment & pe
Definition: filter_step.hpp:33