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biopet.biopet
Commits
63a0ef68
Commit
63a0ef68
authored
Dec 08, 2014
by
Peter van 't Hof
Browse files
Fix for #95
parent
b2a02952
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
63a0ef68
...
...
@@ -97,13 +97,13 @@ object VcfFilter extends ToolCommand {
}
text
(
"Min value of AD field in genotype fields"
)
opt
[
Int
](
"minSamplesPass"
)
unbounded
()
valueName
(
"<int>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
minSamplesPass
=
x
)
}
text
(
"Min number o
p
f samples to pass --minAlternateDepth, --minBamAlternateDepth and --minSampleDepth"
)
}
text
(
"Min number o
f
f samples to pass --minAlternateDepth, --minBamAlternateDepth and --minSampleDepth"
)
opt
[
Int
](
"minBamAlternateDepth"
)
unbounded
()
valueName
(
"<int>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
minBamAlternateDepth
=
x
)
}
// TODO: Convert this to more generic filter
opt
[
String
](
"denovoInSample"
)
maxOccurs
(
1
)
unbounded
()
valueName
(
"<sample>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
denovoInSample
=
x
)
}
text
(
"Only show variants that contain unique alleles in compete set for given sample"
)
}
text
(
"Only show variants that contain unique alleles in comp
l
ete set for given sample"
)
opt
[
String
](
"mustHaveVariant"
)
unbounded
()
valueName
(
"<sample>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
mustHaveVariant
=
x
::
c
.
mustHaveVariant
)
}
text
(
"Given sample must have 1 alternative allele"
)
...
...
@@ -114,7 +114,7 @@ object VcfFilter extends ToolCommand {
opt
[
String
](
"filterHetVarToHomVar"
)
unbounded
()
valueName
(
"<sample:sample>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
filterHetVarToHomVar
=
(
x
.
split
(
":"
)(
0
),
x
.
split
(
":"
)(
1
))
::
c
.
filterHetVarToHomVar
)
}
validate
{
x
=>
if
(
x
.
split
(
":"
).
length
==
2
)
success
else
failure
(
"--filterHetVarToHomVar should be in this format: sample:sample"
)
}
text
(
"If variants in sample 1 are heterogeneous and alternative alleles are homogeneous in sample 2 variants are filterd"
)
}
text
(
"If variants in sample 1 are heterogeneous and alternative alleles are homogeneous in sample 2 variants are filter
e
d"
)
opt
[
Unit
](
"filterRefCalls"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
filterRefCalls
=
true
)
}
text
(
"Filter when there are only ref calls"
)
...
...
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