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vidjil
vidjil
Commits
7e695f73
Commit
7e695f73
authored
Aug 28, 2017
by
Mathieu Giraud
Browse files
algo/vidjil.cpp: remove 'germline_system', streamline code
This was a relic from ancient times.
parent
dcf68c36
Changes
1
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Inline
Side-by-side
algo/vidjil.cpp
View file @
7e695f73
...
...
@@ -315,8 +315,6 @@ int main (int argc, char **argv)
//$$ options: defaults
string
germline_system
=
""
;
list
<
string
>
f_reps_V
;
list
<
string
>
f_reps_D
;
list
<
string
>
f_reps_J
;
...
...
@@ -438,7 +436,6 @@ int main (int argc, char **argv)
case
'V'
:
f_reps_V
.
push_back
(
optarg
);
germline_system
=
"custom"
;
break
;
case
'D'
:
...
...
@@ -448,12 +445,10 @@ int main (int argc, char **argv)
case
'J'
:
f_reps_J
.
push_back
(
optarg
);
germline_system
=
"custom"
;
break
;
case
'g'
:
multi_germline
=
true
;
germline_system
=
"multi"
;
{
string
arg
=
string
(
optarg
);
struct
stat
buffer
;
...
...
@@ -655,7 +650,7 @@ int main (int argc, char **argv)
//$$ options: post-processing+display
if
(
!
germline
_system
.
size
())
if
(
!
multi_
germline
&&
(
!
f_reps_V
.
size
()
||
!
f_reps_J
.
size
())
)
{
cerr
<<
ERROR_STRING
<<
"At least one germline must be given with -g or -V/(-D)/-J."
<<
endl
;
exit
(
1
);
...
...
@@ -693,15 +688,7 @@ int main (int argc, char **argv)
#ifndef NO_SPACED_SEEDS
if
(
kmer_size
==
DEFAULT_K
)
{
if
(
germline_system
.
find
(
"TRA"
)
!=
string
::
npos
)
seed
=
SEED_S13
;
else
if
((
germline_system
.
find
(
"TRB"
)
!=
string
::
npos
)
||
(
germline_system
.
find
(
"IGH"
)
!=
string
::
npos
))
seed
=
SEED_S12
;
else
// TRD, TRG, IGK, IGL, custom, multi
seed
=
SEED_S10
;
seed
=
SEED_S10
;
kmer_size
=
seed_weight
(
seed
);
}
#else
...
...
@@ -861,7 +848,7 @@ int main (int argc, char **argv)
{
// Custom germline
Germline
*
germline
;
germline
=
new
Germline
(
germline_system
,
'X'
,
germline
=
new
Germline
(
"custom"
,
'X'
,
f_reps_V
,
f_reps_D
,
f_reps_J
,
delta_min
,
seed
,
trim_sequences
);
...
...
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