vdj_pipe
pipeline for processing DNA sequence data
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#include <write_sequence_step.hpp>
Public Member Functions | |
VDJ_PIPE_STATIC_STRING_METHOD (comment,"output sequences") Write_seq(Vm_access_single const &vm | |
void | run () |
void | finish () |
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 Attributes | |
File_ostream_variant | fov_ |
std::size_t | n_seq_ |
bool | trim_ |
bool | reverse_ |
bool | skip_empty_ |
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::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::Step_base_single | |
Vm_access_single | vma_ |
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inline |
void vdj_pipe::Write_seq::run | ( | ) |
void vdj_pipe::Write_seq::summary | ( | std::ostream & | os | ) | const |
vdj_pipe::Write_seq::VDJ_PIPE_STATIC_STRING_METHOD | ( | comment | , |
"output sequences" | |||
) | const |
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private |
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boost::property_tree::ptree const Pipe_environment& vdj_pipe::Write_seq::pe |
boost::property_tree::ptree const& vdj_pipe::Write_seq::pt |
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