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biopet.biopet
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cb3dfee1
Commit
cb3dfee1
authored
Sep 09, 2015
by
Peter van 't Hof
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d0887e43
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
...k/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+4
-40
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
View file @
cb3dfee1
...
...
@@ -186,50 +186,14 @@ object VcfStats extends ToolCommand {
c
.
copy
(
generalWiggle
=
x
::
c
.
generalWiggle
,
writeBinStats
=
true
)
}
validate
{
x
=>
if
(
generalWiggleOptions
.
contains
(
x
))
success
else
failure
(
s
"""Nonexistent field $x"""
)
}
text
"""
|Create a wiggle track with bin size <binSize> for any of the following statistics:
|Total
|Biallelic
|ComplexIndel
|Filtered
|FullyDecoded
|Indel
|Mixed
|MNP
|MonomorphicInSamples
|NotFiltered
|PointEvent
|PolymorphicInSamples
|SimpleDeletion
|SimpleInsertion
|SNP
|StructuralIndel
|Symbolic
|SymbolicOrSV
|Variant
"""
.
stripMargin
}
text
s
"""Create a wiggle track with bin size <binSize> for any of the following statistics:
|${generalWiggleOptions.mkString(", ")}"""
.
stripMargin
opt
[
String
](
"genotypeWiggle"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
genotypeWiggle
=
x
::
c
.
genotypeWiggle
,
writeBinStats
=
true
)
}
validate
{
x
=>
if
(
genotypeWiggleOptions
.
contains
(
x
))
success
else
failure
(
s
"""Non-existent field $x"""
)
}
text
"""
|Create a wiggle track with bin size <binSize> for any of the following genotype fields:
|Total
|Het
|HetNonRef
|Hom
|HomRef
|HomVar
|Mixed
|NoCall
|NonInformative
|Available
|Called
|Filtered
|Variant
"""
.
stripMargin
}
text
s
"""Create a wiggle track with bin size <binSize> for any of the following genotype fields:
|${genotypeWiggleOptions.mkString(", ")}"""
.
stripMargin
}
/**
...
...
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