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biopet.biopet
Commits
ece3ce24
Commit
ece3ce24
authored
Nov 17, 2014
by
Peter van 't Hof
Browse files
Added text to args
parent
a36ce065
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
View file @
ece3ce24
...
...
@@ -73,37 +73,37 @@ object BastyGenerateFasta extends ToolCommand {
class
OptParser
extends
AbstractOptParser
{
opt
[
File
](
'V'
,
"inputVcf"
)
unbounded
()
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
inputVcf
=
x
)
}
}
text
(
"vcf file, needed for outputVariants and outputConsensusVariants"
)
opt
[
File
](
"bamFile"
)
unbounded
()
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
bamFile
=
x
)
}
opt
[
File
](
"outputVariants"
)
unbounded
()
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
}
text
(
"bam file, needed for outputConsensus and outputConsensusVariants"
)
opt
[
File
](
"outputVariants"
)
maxOccurs
(
1
)
unbounded
()
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
outputVariants
=
x
)
}
opt
[
File
](
"outputConsensus"
)
unbounded
()
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
}
text
(
"fasta with only variants from vcf file"
)
opt
[
File
](
"outputConsensus"
)
maxOccurs
(
1
)
unbounded
()
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
outputConsensus
=
x
)
}
opt
[
File
](
"outputConsensusVariants"
)
unbounded
()
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
}
text
(
"Consensus fasta from bam, always reference bases else 'N'"
)
opt
[
File
](
"outputConsensusVariants"
)
maxOccurs
(
1
)
unbounded
()
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
outputConsensusVariants
=
x
)
}
}
text
(
"Consensus fasta from bam with variants from vcf file, always reference bases else 'N'"
)
opt
[
Unit
](
"snpsOnly"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
snpsOnly
=
true
)
}
}
text
(
"Only use snps from vcf file"
)
opt
[
String
](
"sampleName"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
sampleName
=
x
)
}
}
text
(
"Sample name in vcf file"
)
opt
[
String
](
"outputName"
)
required
()
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
outputName
=
x
)
}
}
text
(
"Output name in fasta file header"
)
opt
[
Int
](
"minAD"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
minAD
=
x
)
}
}
text
(
"min AD value in vcf file for sample"
)
opt
[
Int
](
"minDepth"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
minDepth
=
x
)
}
}
text
(
"min detp in bam file"
)
opt
[
File
](
"reference"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
reference
=
x
)
}
}
text
(
"Indexed reference fasta file"
)
}
protected
var
cmdArgs
:
Args
=
_
...
...
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