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biopet.biopet
Commits
4982a72c
Commit
4982a72c
authored
May 23, 2016
by
Peter van 't Hof
Browse files
Style fix
parent
9b8ddc12
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
4982a72c
...
...
@@ -33,6 +33,11 @@ object VcfFilter extends ToolCommand {
}
}
case
class
BooleanArgs
(
uniqueOnly
:
Boolean
=
false
,
sharedOnly
:
Boolean
=
false
,
filterRefCalls
:
Boolean
=
false
,
filterNoCalls
:
Boolean
=
false
)
case
class
Args
(
inputVcf
:
File
=
null
,
outputVcf
:
File
=
null
,
invertedOutputVcf
:
Option
[
File
]
=
None
,
...
...
@@ -49,14 +54,12 @@ object VcfFilter extends ToolCommand {
trioCompound
:
List
[
Trio
]
=
Nil
,
deNovoTrio
:
List
[
Trio
]
=
Nil
,
trioLossOfHet
:
List
[
Trio
]
=
Nil
,
booleanArgs
:
BooleanArgs
=
BooleanArgs
(),
diffGenotype
:
List
[(
String
,
String
)]
=
Nil
,
filterHetVarToHomVar
:
List
[(
String
,
String
)]
=
Nil
,
uniqueOnly
:
Boolean
=
false
,
sharedOnly
:
Boolean
=
false
,
filterRefCalls
:
Boolean
=
false
,
filterNoCalls
:
Boolean
=
false
,
iDset
:
Set
[
String
]
=
Set
(),
minGenomeQuality
:
Int
=
0
)
extends
AbstractArgs
minGenomeQuality
:
Int
=
0
)
extends
AbstractArgs
{
}
class
OptParser
extends
AbstractOptParser
{
opt
[
File
](
'I'
,
"inputVcf"
)
required
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
...
...
@@ -116,16 +119,16 @@ object VcfFilter extends ToolCommand {
}
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 filtered"
opt
[
Unit
](
"filterRefCalls"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
filterRefCalls
=
true
)
c
.
copy
(
booleanArgs
=
c
.
booleanArgs
.
copy
(
filterRefCalls
=
true
)
)
}
text
"Filter when there are only ref calls"
opt
[
Unit
](
"filterNoCalls"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
filterNoCalls
=
true
)
c
.
copy
(
booleanArgs
=
c
.
booleanArgs
.
copy
(
filterNoCalls
=
true
)
)
}
text
"Filter when there are only no calls"
opt
[
Unit
](
"uniqueOnly"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
uniqueOnly
=
true
)
c
.
copy
(
booleanArgs
=
c
.
booleanArgs
.
copy
(
uniqueOnly
=
true
)
)
}
text
"Filter when there more then 1 sample have this variant"
opt
[
Unit
](
"sharedOnly"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
sharedOnly
=
true
)
c
.
copy
(
booleanArgs
=
c
.
booleanArgs
.
copy
(
sharedOnly
=
true
)
)
}
text
"Filter when not all samples have this variant"
opt
[
Double
](
"minQualScore"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
minQualScore
=
Some
(
x
))
...
...
@@ -167,10 +170,10 @@ object VcfFilter extends ToolCommand {
var
counterLeft
=
0
for
(
record
<-
reader
)
{
if
(
cmdArgs
.
minQualScore
.
map
(
minQualscore
(
record
,
_
)).
getOrElse
(
true
)
&&
(!
cmdArgs
.
filterRefCalls
||
hasNonRefCalls
(
record
))
&&
(!
cmdArgs
.
filterNoCalls
||
hasCalls
(
record
))
&&
(!
cmdArgs
.
uniqueOnly
||
hasUniqeSample
(
record
))
&&
(!
cmdArgs
.
sharedOnly
||
allSamplesVariant
(
record
))
&&
(!
cmdArgs
.
booleanArgs
.
filterRefCalls
||
hasNonRefCalls
(
record
))
&&
(!
cmdArgs
.
booleanArgs
.
filterNoCalls
||
hasCalls
(
record
))
&&
(!
cmdArgs
.
booleanArgs
.
uniqueOnly
||
hasUniqeSample
(
record
))
&&
(!
cmdArgs
.
booleanArgs
.
sharedOnly
||
allSamplesVariant
(
record
))
&&
hasMinTotalDepth
(
record
,
cmdArgs
.
minTotalDepth
)
&&
hasMinSampleDepth
(
record
,
cmdArgs
.
minSampleDepth
,
cmdArgs
.
minSamplesPass
)
&&
minAlternateDepth
(
record
,
cmdArgs
.
minAlternateDepth
,
cmdArgs
.
minSamplesPass
)
&&
...
...
@@ -246,12 +249,12 @@ object VcfFilter extends ToolCommand {
/** Checks if there is a variant in only 1 sample */
def
hasUniqeSample
(
record
:
VariantContext
)
:
Boolean
=
{
record
.
getGenotypes
.
count
(
_
.
getAlleles
.
exists
(
a
=>
a
.
isNonReference
&&
!
a
.
isNoCall
))
==
1
record
.
getGenotypes
.
count
(
g
=>
!
g
.
isNonInformative
&&
g
.
getAlleles
.
exists
(
a
=>
a
.
isNonReference
&&
!
a
.
isNoCall
))
==
1
}
/** Checks if all samples are a variant */
def
allSamplesVariant
(
record
:
VariantContext
)
:
Boolean
=
{
record
.
getGenotypes
.
forall
(
_
.
getAlleles
.
exists
(
a
=>
a
.
isNonReference
&&
!
a
.
isNoCall
))
record
.
getGenotypes
.
forall
(
g
=>
!
g
.
isNonInformative
&&
g
.
getAlleles
.
exists
(
a
=>
a
.
isNonReference
&&
!
a
.
isNoCall
))
}
/** returns true when DP INFO field is atleast the given value */
...
...
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