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gad-public
vihgo
Commits
1efacb84
Commit
1efacb84
authored
Jan 22, 2021
by
Yannis Duffourd
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Adding new option to support full cs sequence writing
parent
42b3a014
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1 changed file
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10 additions
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2 deletions
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main.cpp
cpp/main.cpp
+10
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cpp/main.cpp
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1efacb84
...
...
@@ -27,6 +27,7 @@ int main(int argc, char* argv[])
cerr
<<
"Starting Main"
<<
endl
;
bool
countStop
=
false
;
bool
fullCS
=
false
;
int
currentThread
=
0
;
int
depthThreshold
;
...
...
@@ -56,7 +57,7 @@ int main(int argc, char* argv[])
(
"output,o"
,
po
::
value
<
string
>
(
&
outputFile
),
"output result file variants."
)
(
"logFile,l"
,
po
::
value
<
string
>
(
&
logFile
),
"Log file output."
)
(
"codon,c"
,
po
::
value
<
string
>
(
&
codonResultFile
),
"output result file variants."
)
(
"consensus,C"
,
po
::
value
<
string
>
(
&
csFile
),
"Consensus sequence file (fasta)."
)
(
"consensus,C"
,
po
::
value
<
string
>
(
&
csFile
),
"Consensus sequence file
to be written
(fasta)."
)
(
"integrase,I"
,
po
::
value
<
string
>
(
&
integraseFile
),
"File annotation for integrase prot."
)
(
"rt,R"
,
po
::
value
<
string
>
(
&
rtFile
)
,
"File annotation for retrotranscriptase prot."
)
...
...
@@ -69,6 +70,7 @@ int main(int argc, char* argv[])
(
"ratio,a"
,
po
::
value
<
double
>
(
&
ratioThreshold
)
->
default_value
(
0.1
)
,
"Minimum ratio of alt reads to consider a mutation. (optional)"
)
(
"pvalue,p"
,
po
::
value
<
double
>
(
&
pvalueThreshold
)
->
default_value
(
0.05
)
,
"pvalue threshold from FET to consider a mutation. (optional)"
)
(
"stop,s"
,
"Activate stop codon detction."
)
(
"fullcs,f"
,
"Write full genome consensus instead of gene by gene."
)
(
"thread,t"
,
po
::
value
<
int
>
(
&
nbThread
)
->
default_value
(
50
),
"Number of thread to use. (NYI)"
)
(
"loglevel,L"
,
po
::
value
<
int
>
(
&
loggingLevel
)
->
default_value
(
1
),
"Logging level."
);
...
...
@@ -180,7 +182,13 @@ int main(int argc, char* argv[])
countStop
=
true
;
}
Vihgo
*
App
=
new
Vihgo
(
bamFile
,
geneFile
,
rtFile
,
integraseFile
,
proteaseFile
,
referenceFile
,
outputFile
,
codonResultFile
,
csFile
,
inRunControlBam
,
depthThreshold
,
nbThread
,
loggingLevel
,
ratioThreshold
,
pvalueThreshold
,
countStop
);
if
(
vm
.
count
(
"fullcs"
)
)
{
fullCS
=
true
;
}
Vihgo
*
App
=
new
Vihgo
(
bamFile
,
geneFile
,
rtFile
,
integraseFile
,
proteaseFile
,
referenceFile
,
outputFile
,
codonResultFile
,
csFile
,
inRunControlBam
,
depthThreshold
,
nbThread
,
loggingLevel
,
ratioThreshold
,
pvalueThreshold
,
countStop
,
fullCS
);
App
->
mainLoop
();
...
...
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