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vidjil
vidjil
Commits
fb472053
Commit
fb472053
authored
Oct 09, 2014
by
Mathieu Giraud
Browse files
vidjil.cpp: default command is '-c clones' (renamed CMD_CLONES)
parent
612230b2
Changes
1
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Inline
Side-by-side
algo/vidjil.cpp
View file @
fb472053
...
...
@@ -75,11 +75,11 @@
#define RATIO_READS_CLONE 0.0
#define COMMAND_WINDOWS "windows"
#define COMMAND_
ANALYSI
S "clones"
#define COMMAND_
CLONE
S "clones"
#define COMMAND_SEGMENT "segment"
#define COMMAND_GERMLINES "germlines"
enum
{
CMD_WINDOWS
,
CMD_
ANALYSI
S
,
CMD_SEGMENT
,
CMD_GERMLINES
}
;
enum
{
CMD_WINDOWS
,
CMD_
CLONE
S
,
CMD_SEGMENT
,
CMD_GERMLINES
}
;
#define OUT_DIR "./out/"
#define CLONES_FILENAME "clones.vdj.fa"
...
...
@@ -135,8 +135,8 @@ void usage(char *progname)
cerr
<<
"Usage: "
<<
progname
<<
" [options] <reads.fa>"
<<
endl
<<
endl
;
cerr
<<
"Command selection"
<<
endl
<<
" -c <command>
\t
"
<<
COMMAND_WINDOWS
<<
"
\t
window extracting
(default)
"
<<
endl
<<
"
\t\t
"
<<
COMMAND_
ANALYSI
S
<<
"
\t
clone
analysis
"
<<
endl
<<
" -c <command>
\t
"
<<
COMMAND_WINDOWS
<<
"
\t
window extracting"
<<
endl
<<
"
\t\t
"
<<
COMMAND_
CLONE
S
<<
"
\t
clone
gathering (default)
"
<<
endl
<<
"
\t\t
"
<<
COMMAND_SEGMENT
<<
"
\t
V(D)J segmentation (not recommended)"
<<
endl
<<
"
\t\t
"
<<
COMMAND_GERMLINES
<<
"
\t
discover all germlines"
<<
endl
<<
endl
...
...
@@ -210,7 +210,6 @@ void usage(char *progname)
<<
endl
<<
"Examples (see doc/README)"
<<
endl
<<
" "
<<
progname
<<
" -G germline/IGH -d data/Stanford_S22.fasta"
<<
endl
<<
" "
<<
progname
<<
" -c clones -G germline/IGH -r 5 -d data/Stanford_S22.fasta"
<<
endl
<<
" "
<<
progname
<<
" -c segment -G germline/IGH -d data/Stanford_S22.fasta # (only for testing)"
<<
endl
<<
" "
<<
progname
<<
" -c germlines data/Stanford_S22.fasta"
<<
endl
...
...
@@ -259,7 +258,7 @@ int main (int argc, char **argv)
int
segment_D
=
0
;
int
verbose
=
0
;
int
command
=
CMD_
WINDOW
S
;
int
command
=
CMD_
CLONE
S
;
int
max_clones
=
MAX_CLONES
;
int
min_reads_clone
=
MIN_READS_CLONE
;
...
...
@@ -321,8 +320,8 @@ int main (int argc, char **argv)
detailed_cluster_analysis
=
false
;
break
;
case
'c'
:
if
(
!
strcmp
(
COMMAND_
ANALYSI
S
,
optarg
))
command
=
CMD_
ANALYSI
S
;
if
(
!
strcmp
(
COMMAND_
CLONE
S
,
optarg
))
command
=
CMD_
CLONE
S
;
else
if
(
!
strcmp
(
COMMAND_SEGMENT
,
optarg
))
command
=
CMD_SEGMENT
;
else
if
(
!
strcmp
(
COMMAND_WINDOWS
,
optarg
))
...
...
@@ -553,7 +552,7 @@ int main (int argc, char **argv)
switch
(
command
)
{
case
CMD_WINDOWS
:
cout
<<
"Extracting windows"
<<
endl
;
break
;
case
CMD_
ANALYSI
S
:
cout
<<
"Analysing clones"
<<
endl
;
case
CMD_
CLONE
S
:
cout
<<
"Analysing clones"
<<
endl
;
break
;
case
CMD_SEGMENT
:
cout
<<
"Segmenting V(D)J"
<<
endl
;
break
;
...
...
@@ -763,7 +762,7 @@ int main (int argc, char **argv)
////////////////////////////////////////
// CLONE ANALYSIS //
////////////////////////////////////////
if
(
command
==
CMD_
ANALYSI
S
||
command
==
CMD_WINDOWS
)
{
if
(
command
==
CMD_
CLONE
S
||
command
==
CMD_WINDOWS
)
{
//////////////////////////////////
cout
<<
"# seed = "
<<
seed
<<
","
;
...
...
@@ -882,7 +881,7 @@ int main (int argc, char **argv)
list
<
pair
<
float
,
int
>
>
norm_list
=
compute_normalization_list
(
windowsStorage
->
getMap
(),
normalization
,
nb_segmented
);
if
(
command
==
CMD_
ANALYSI
S
)
{
if
(
command
==
CMD_
CLONE
S
)
{
//////////////////////////////////
//$$ min_reads_clone (ou label)
...
...
@@ -1163,7 +1162,7 @@ int main (int argc, char **argv)
}
// endif (clones_windows.size() > 0)
}
// end if (command == CMD_
ANALYSI
S)
}
// end if (command == CMD_
CLONE
S)
//$$ .json output: json_data_segment
string
f_json
=
out_dir
+
prefix_filename
+
"vidjil"
+
JSON_SUFFIX
;
// TODO: retrieve basename from f_reads instead of "vidjil"
...
...
@@ -1240,7 +1239,7 @@ int main (int argc, char **argv)
cout
<<
"* WARNING: vidjil was run with '-c segment' option"
<<
endl
<<
"* Vidjil purpose is to extract very quickly windows overlapping the CDR3"
<<
endl
<<
"*
or
to gather reads into clones (-c clones), and not to provide an accurate V(D)J segmentation."
<<
endl
<<
"*
and
to gather reads into clones (-c clones), and not to provide an accurate V(D)J segmentation."
<<
endl
<<
"* The following segmentations are slow to compute and are provided only for convenience."
<<
endl
<<
"* They should be checked with other softwares such as IgBlast, iHHMune-align or IMGT/V-QUEST."
<<
endl
;
...
...
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