vdj_pipe
pipeline for processing DNA sequence data
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include
vdj_pipe
pipe_paired_read.hpp
Go to the documentation of this file.
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#ifndef PIPE_PAIRED_READ_HPP_
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#define PIPE_PAIRED_READ_HPP_
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#include <string>
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#include "boost/property_tree/ptree_fwd.hpp"
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#include "
vdj_pipe/config.hpp
"
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#include "
vdj_pipe/exception.hpp
"
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#include "
vdj_pipe/pipe_environment.hpp
"
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#include "
vdj_pipe/value_map_access_paired.hpp
"
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namespace
vdj_pipe
{
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class
Seq_file;
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class
VDJ_PIPE_DECL
Pipe_paired_read
{
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public
:
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struct
Err
:
public
base_exception
{};
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explicit
Pipe_paired_read
(
boost::property_tree::ptree
const
& pt);
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void
run();
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Pipe_environment
const
&
pe
()
const
{
return
pe_;}
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private
:
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Vm_access_paired
vma_
;
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Pipe_environment
pe_
;
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void
check()
const
;
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void
process_fastq(
Seq_file_entry
const
& sfe);
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void
process_fasta_qual(
Seq_file_entry
const
& sfe);
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void
store_records(
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Seq_qual_record
const
& r_fwd,
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Seq_qual_record
const
& r_rev
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);
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};
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}
//namespace vdj_pipe
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#endif
/* PIPE_PAIRED_READ_HPP_ */
vdj_pipe::Pipe_paired_read::Err
Definition:
pipe_paired_read.hpp:23
vdj_pipe::Pipe_paired_read::pe
Pipe_environment const & pe() const
Definition:
pipe_paired_read.hpp:26
pipe_environment.hpp
config.hpp
vdj_pipe::Vm_access_paired
Access to value map for paired read pipeline and processing steps.
Definition:
value_map_access_paired.hpp:16
vdj_pipe::Seq_qual_record
Definition:
sequence_record.hpp:77
vdj_pipe
Main namespace of vdj_pipe library.
Definition:
keywords_variable.hpp:11
vdj_pipe::Pipe_environment
Definition:
pipe_environment.hpp:26
VDJ_PIPE_DECL
#define VDJ_PIPE_DECL
Definition:
config.hpp:23
vdj_pipe::Seq_file_entry
Definition:
sequence_file_entry.hpp:26
value_map_access_paired.hpp
vdj_pipe::Pipe_paired_read::pe_
Pipe_environment pe_
Definition:
pipe_paired_read.hpp:30
exception.hpp
vdj_pipe::base_exception
Definition:
exception.hpp:23
vdj_pipe::Pipe_paired_read
process paired reads with external MIDs
Definition:
pipe_paired_read.hpp:21
vdj_pipe::test::ptree
bpt::ptree ptree
Definition:
processing_step_utils.hpp:19
vdj_pipe::Pipe_paired_read::vma_
Vm_access_paired vma_
Definition:
pipe_paired_read.hpp:29
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