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biopet.biopet
Commits
c538587a
Commit
c538587a
authored
May 11, 2015
by
Peter van 't Hof
Browse files
Added calledIn option
parent
c6aaac86
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
c538587a
...
...
@@ -69,9 +69,10 @@ object VcfFilter extends ToolCommand {
minSampleDepth
:
Int
=
-
1
,
minTotalDepth
:
Int
=
-
1
,
minAlternateDepth
:
Int
=
-
1
,
minSamplesPass
:
Int
=
0
,
minSamplesPass
:
Int
=
1
,
minBamAlternateDepth
:
Int
=
0
,
mustHaveVariant
:
List
[
String
]
=
Nil
,
calledIn
:
List
[
String
]
=
Nil
,
deNovoInSample
:
String
=
null
,
deNovoTrio
:
List
[
Trio
]
=
Nil
,
trioLossOfHet
:
List
[
Trio
]
=
Nil
,
...
...
@@ -118,6 +119,9 @@ object VcfFilter extends ToolCommand {
opt
[
String
](
"mustHaveVariant"
)
unbounded
()
valueName
(
"<sample>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
mustHaveVariant
=
x
::
c
.
mustHaveVariant
)
}
text
(
"Given sample must have 1 alternative allele"
)
opt
[
String
](
"calledIn"
)
unbounded
()
valueName
(
"<sample>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
calledIn
=
x
::
c
.
calledIn
)
}
text
(
"Must be called in this sample"
)
opt
[
String
](
"diffGenotype"
)
unbounded
()
valueName
(
"<sample:sample>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
diffGenotype
=
(
x
.
split
(
":"
)(
0
),
x
.
split
(
":"
)(
1
))
::
c
.
diffGenotype
)
}
validate
{
x
=>
if
(
x
.
split
(
":"
).
length
==
2
)
success
else
failure
(
"--notSameGenotype should be in this format: sample:sample"
)
...
...
@@ -180,6 +184,7 @@ object VcfFilter extends ToolCommand {
minAlternateDepth
(
record
)
&&
minBamAlternateDepth
(
record
,
header
)
&&
mustHaveVariant
(
record
)
&&
called
(
record
)
&&
notSameGenotype
(
record
)
&&
filterHetVarToHomVar
(
record
)
&&
denovoInSample
(
record
)
&&
...
...
@@ -200,6 +205,11 @@ object VcfFilter extends ToolCommand {
logger
.
info
(
"Done"
)
}
def
called
(
record
:
VariantContext
)
:
Boolean
=
{
if
(!
commandArgs
.
calledIn
.
forall
(
record
.
getGenotype
(
_
).
isCalled
))
false
else
true
}
def
minQualscore
(
record
:
VariantContext
)
:
Boolean
=
{
if
(
commandArgs
.
minQualScore
.
isEmpty
)
return
true
record
.
getPhredScaledQual
>=
commandArgs
.
minQualScore
.
get
...
...
@@ -302,8 +312,14 @@ object VcfFilter extends ToolCommand {
val
fatherCount
=
father
.
countAllele
(
allele
)
val
motherCount
=
mother
.
countAllele
(
allele
)
if
(!
onlyLossHet
&&
childCount
==
1
&&
fatherCount
==
0
&&
motherCount
==
0
)
return
true
else
if
(
childCount
==
2
&&
(
fatherCount
==
0
||
motherCount
==
0
))
return
true
if
(
onlyLossHet
)
{
if
(
childCount
==
2
&&
(
(
fatherCount
==
2
&&
motherCount
==
0
)
||
(
fatherCount
==
0
&&
motherCount
==
2
)))
return
true
}
else
{
if
(
childCount
==
1
&&
fatherCount
==
0
&&
motherCount
==
0
)
return
true
else
if
(
childCount
==
2
&&
(
fatherCount
==
0
||
motherCount
==
0
))
return
true
}
}
}
return
trios
.
isEmpty
...
...
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