vdj_pipe
pipeline for processing DNA sequence data
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#include <filter_step.hpp>
Public Member Functions | |
VDJ_PIPE_STATIC_STRING_METHOD (comment,"discard reads that contain a quality score lower than minimal") Min_quality_filter(Vm_access_single const &vma | |
void | run () |
void | finish () |
Public Member Functions inherited from vdj_pipe::detail::Filter_base | |
void | summary (std::ostream &os) const |
Public Member Functions inherited from vdj_pipe::detail::Step_base_single | |
void | reset_access (Value_ids_single const &ids) |
Public Member Functions inherited from vdj_pipe::detail::Step_base | |
char | delimiter () const |
Step_base (boost::property_tree::ptree const &pt, Pipe_environment const &pe) | |
void | summary (std::ostream &) const |
Public Attributes | |
boost::property_tree::ptree const & | pt |
boost::property_tree::ptree const Pipe_environment & | pe |
Private Types | |
typedef Qual_record::quality::value_type | value_type |
Private Attributes | |
value_type | min_ |
Additional Inherited Members | |
Public Types inherited from vdj_pipe::detail::Step_base_single | |
typedef Vm_access_single | vma_type |
Public Types inherited from vdj_pipe::detail::Step_base | |
typedef Seq_record::sequence | seq_type |
typedef Qual_record::quality | qual_type |
Protected Member Functions inherited from vdj_pipe::detail::Filter_base | |
VDJ_PIPE_KEYWORD_STRUCT (kwds,(passed_name)) | |
Filter_base (vma_type const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe) | |
void | pass (const bool b) |
Protected Member Functions inherited from vdj_pipe::detail::Step_base_single | |
Step_base_single (vma_type const &vma, boost::property_tree::ptree const &pt, Pipe_environment const &pe) | |
Protected Attributes inherited from vdj_pipe::detail::Filter_base | |
std::size_t | nf_ |
Val_id | pass_id_ |
Protected Attributes inherited from vdj_pipe::detail::Step_base_single | |
Vm_access_single | vma_ |
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inline |
void vdj_pipe::Min_quality_filter::run | ( | ) |
vdj_pipe::Min_quality_filter::VDJ_PIPE_STATIC_STRING_METHOD | ( | comment | , |
"discard reads that contain a quality score lower than minimal" | |||
) | const |
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private |
boost::property_tree::ptree const Pipe_environment& vdj_pipe::Min_quality_filter::pe |
boost::property_tree::ptree const& vdj_pipe::Min_quality_filter::pt |