vdj_pipe
pipeline for processing DNA sequence data
Main Page
Related Pages
Namespaces
Classes
Files
File List
File Members
include
vdj_pipe
pipe_single_read.hpp
Go to the documentation of this file.
1
7
#ifndef PIPE_SINGLE_READ_HPP_
8
#define PIPE_SINGLE_READ_HPP_
9
#include <string>
10
#include "boost/property_tree/ptree_fwd.hpp"
11
#include "
vdj_pipe/config.hpp
"
12
#include "
vdj_pipe/pipe_environment.hpp
"
13
#include "
vdj_pipe/value_map_access_single.hpp
"
14
15
namespace
vdj_pipe
{
16
class
Seq_file;
17
20
class
VDJ_PIPE_DECL
Pipe_single_read
{
21
public
:
22
struct
Err
:
public
base_exception
{};
23
explicit
Pipe_single_read
(
boost::property_tree::ptree
const
& pt);
24
void
run();
25
Pipe_environment
const
&
pe
()
const
{
return
pe_;}
26
27
private
:
28
Vm_access_single
vma_
;
29
Pipe_environment
pe_
;
30
31
void
process_fastq(
Seq_file_entry
const
& sfe);
32
void
process_fasta_qual(
Seq_file_entry
const
& sfe);
33
void
check()
const
;
34
};
35
36
}
//namespace vdj_pipe
37
#endif
/* PIPE_SINGLE_READ_HPP_ */
vdj_pipe::Pipe_single_read::Err
Definition:
pipe_single_read.hpp:22
value_map_access_single.hpp
vdj_pipe::Pipe_single_read::vma_
Vm_access_single vma_
Definition:
pipe_single_read.hpp:28
vdj_pipe::Vm_access_single
Definition:
value_map_access_single.hpp:16
vdj_pipe::Pipe_single_read::pe_
Pipe_environment pe_
Definition:
pipe_single_read.hpp:29
pipe_environment.hpp
config.hpp
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
vdj_pipe::Pipe_single_read
Definition:
pipe_single_read.hpp:20
vdj_pipe::Pipe_single_read::pe
Pipe_environment const & pe() const
Definition:
pipe_single_read.hpp:25
vdj_pipe::base_exception
Definition:
exception.hpp:23
vdj_pipe::test::ptree
bpt::ptree ptree
Definition:
processing_step_utils.hpp:19
Generated by
1.8.11