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CorrelationMatrixCreatorApplicationParallel.cpp
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Created
Fri, May 3, 20:00
Size
7 KB
Mime Type
text/x-c
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Sun, May 5, 20:00 (2 d)
Engine
blob
Format
Raw Data
Handle
17449775
Attached To
R8820 scATAC-seq
CorrelationMatrixCreatorApplicationParallel.cpp
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#include <CorrelationMatrixCreatorApplication.hpp>
#include <MatrixCreator.hpp>
// MatrixCreator::methods
#include <CorrelationMatrixCreator.hpp>
#include <boost/program_options.hpp>
#include <iostream>
#include <string>
#include <stdexcept>
// std::invalid_argument
namespace
po
=
boost
::
program_options
;
// the valid values for --method option
std
::
string
method_read
=
"read"
;
std
::
string
method_read_atac
=
"read_atac"
;
std
::
string
method_fragment
=
"fragment"
;
std
::
string
method_fragment_center
=
"fragment_center"
;
CorrelationMatrixCreatorApplication
::
CorrelationMatrixCreatorApplication
(
int
argn
,
char
**
argv
)
:
file_bed
(
""
),
file_bam
(
""
),
from
(
0
),
to
(
0
),
bin_size
(
0
),
method
(
MatrixCreator
::
FRAGMENT
),
runnable
(
true
),
n_threads
(
1
)
{
// parse command line options and set the fields
this
->
parseOptions
(
argn
,
argv
)
;
}
int
CorrelationMatrixCreatorApplication
::
run
()
{
if
(
this
->
runnable
)
{
CorrelationMatrixCreator
mc
(
this
->
file_bed
,
this
->
file_bam
,
this
->
file_bai
,
this
->
from
,
this
->
to
,
this
->
bin_size
,
this
->
method
,
this
->
n_threads
)
;
std
::
cout
<<
mc
.
create_matrix
()
<<
std
::
endl
;
return
EXIT_SUCCESS
;
}
else
{
return
EXIT_FAILURE
;
}
}
void
CorrelationMatrixCreatorApplication
::
parseOptions
(
int
argn
,
char
**
argv
)
{
// no option to parse
if
(
argv
==
nullptr
)
{
std
::
string
message
=
"no options to parse!"
;
throw
std
::
invalid_argument
(
message
)
;
}
// help messages
std
::
string
desc_msg
=
"
\n
"
"CorrelationMatrixCreator is an application that creates a "
"count matrix from a BED file and a BAM file and returnes it "
"through stdout.
\n
"
"The matrix contains one row per reference region present in the "
"BED file. The region center is computed and then a region covering the "
"interval [from,to] is build around the middle and divided into "
"equally sized bins. Finally, each bin is assigned the number of "
"target present in the BAM file that are mapped at that position.
\n\n
"
;
std
::
string
opt_help_msg
=
"Produces this help message."
;
std
::
string
opt_bed_msg
=
"The path to the BED file containing the references"
;
std
::
string
opt_bam_msg
=
"The path to the BAM file containing the targets"
;
std
::
string
opt_bai_msg
=
"The path to the BAM index file of the BAM file containing the targets"
;
std
::
string
opt_from_msg
=
"The upstream limit - in relative coordinate - of the region to build "
"around each reference center."
;
std
::
string
opt_to_msg
=
"The downstream limit - in relative coordinate - of the region to build "
"around each reference center."
;
std
::
string
opt_thread_msg
=
"The number of threads to use."
;
std
::
string
opt_binsize_msg
=
"The size of the bins."
;
char
tmp
[
4096
]
;
sprintf
(
tmp
,
"How the data in the BAM file should be handled when computing "
"the number of counts in each bin.
\n
"
"
\t\"
%s
\"
uses each position within the reads (by default)
\n
"
"
\t\"
%s
\"
uses only the insertion site for ATAC-seq data
\n
"
"
\t\"
%s
\"
uses each position within the fragments
\n
"
"
\t\"
%s
\"
uses only the fragment central positions
\n
"
,
method_read
.
c_str
(),
method_read_atac
.
c_str
(),
method_fragment
.
c_str
(),
method_fragment_center
.
c_str
())
;
std
::
string
opt_method_msg
=
tmp
;
// option parser
boost
::
program_options
::
variables_map
vm
;
boost
::
program_options
::
options_description
desc
(
desc_msg
)
;
std
::
string
method
(
method_read
)
;
desc
.
add_options
()
(
"help,h"
,
opt_help_msg
.
c_str
())
(
"bed"
,
po
::
value
<
std
::
string
>
(
&
(
this
->
file_bed
)),
opt_bed_msg
.
c_str
())
(
"bam"
,
po
::
value
<
std
::
string
>
(
&
(
this
->
file_bam
)),
opt_bam_msg
.
c_str
())
(
"bai"
,
po
::
value
<
std
::
string
>
(
&
(
this
->
file_bai
)),
opt_bai_msg
.
c_str
())
(
"from,f"
,
po
::
value
<
int
>
(
&
(
this
->
from
)),
opt_from_msg
.
c_str
())
(
"to,t"
,
po
::
value
<
int
>
(
&
(
this
->
to
)),
opt_to_msg
.
c_str
())
(
"binSize,b"
,
po
::
value
<
int
>
(
&
(
this
->
bin_size
)),
opt_binsize_msg
.
c_str
())
(
"method,m"
,
po
::
value
<
std
::
string
>
(
&
(
method
)),
opt_method_msg
.
c_str
())
(
"parallel,p"
,
po
::
value
<
size_t
>
(
&
(
this
->
n_threads
)),
opt_thread_msg
.
c_str
())
;
// parse
try
{
po
::
store
(
po
::
parse_command_line
(
argn
,
argv
,
desc
),
vm
)
;
po
::
notify
(
vm
)
;
}
catch
(
std
::
invalid_argument
&
e
)
{
std
::
string
msg
=
std
::
string
(
"Error! Invalid option given!
\n
"
)
+
std
::
string
(
e
.
what
())
;
throw
std
::
invalid_argument
(
msg
)
;
}
catch
(...)
{
throw
std
::
invalid_argument
(
"An unknown error occured while parsing the options"
)
;
}
bool
help
=
vm
.
count
(
"help"
)
;
// checks unproper option settings
if
(
this
->
file_bed
==
""
and
(
not
help
))
{
std
::
string
msg
(
"Error! No BED file was given (--bed)!"
)
;
throw
std
::
invalid_argument
(
msg
)
;
}
else
if
(
this
->
file_bam
==
""
and
(
not
help
))
{
std
::
string
msg
(
"Error! No BAM file was given (--bam)!"
)
;
throw
std
::
invalid_argument
(
msg
)
;
}
else
if
(
this
->
file_bam
==
""
and
(
not
help
))
{
std
::
string
msg
(
"Error! No BAM index file was given (--bai)!"
)
;
throw
std
::
invalid_argument
(
msg
)
;
}
else
if
(
this
->
from
==
0
and
this
->
to
==
0
and
(
not
help
))
{
std
::
string
msg
(
"Error! No range given (--from and --to)!"
)
;
throw
std
::
invalid_argument
(
msg
)
;
}
else
if
(
this
->
from
>=
this
->
to
and
(
not
help
))
{
std
::
string
msg
(
"Error! from shoud be smaller than to (--from and --to)!"
)
;
throw
std
::
invalid_argument
(
msg
)
;
}
else
if
(
this
->
bin_size
<=
0
and
(
not
help
))
{
std
::
string
msg
(
"Error! bin size should be bigger than 0 (--binSize)!"
)
;
throw
std
::
invalid_argument
(
msg
)
;
}
else
if
(
method
!=
method_read
and
method
!=
method_read_atac
and
method
!=
method_fragment
and
method
!=
method_fragment_center
)
{
char
msg
[
4096
]
;
sprintf
(
msg
,
"Error! method should be %s, %s, %s or %s (--method)"
,
method_read
.
c_str
(),
method_read_atac
.
c_str
(),
method_fragment
.
c_str
(),
method_fragment_center
.
c_str
())
;
throw
std
::
invalid_argument
(
msg
)
;
}
else
if
(
this
->
n_threads
==
0
)
{
std
::
string
msg
(
"Error! at least one thread should be used (--parallel)!"
)
;
throw
std
::
invalid_argument
(
msg
)
;
}
// set method
if
(
method
==
method_read
)
{
this
->
method
=
MatrixCreator
::
READ
;
}
else
if
(
method
==
method_read_atac
)
{
this
->
method
=
MatrixCreator
::
READ_ATAC
;
}
else
if
(
method
==
method_fragment
)
{
this
->
method
=
MatrixCreator
::
FRAGMENT
;
}
else
if
(
method
==
method_fragment_center
)
{
this
->
method
=
MatrixCreator
::
FRAGMENT_CENTER
;
}
// help invoked, run() cannot be invoked
if
(
help
)
{
std
::
cout
<<
desc
<<
std
::
endl
;
this
->
runnable
=
false
;
return
;
}
// everything fine, run() can be called
else
{
this
->
runnable
=
true
;
return
;
}
}
int
main
(
int
argn
,
char
**
argv
)
{
CorrelationMatrixCreatorApplication
app
(
argn
,
argv
)
;
return
app
.
run
()
;
}
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