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biopet.biopet
Commits
9c002013
Commit
9c002013
authored
Apr 11, 2016
by
Peter van 't Hof
Browse files
Fixed bug
parent
180bb97e
Changes
1
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public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
9c002013
...
...
@@ -263,7 +263,7 @@ object VcfFilter extends ToolCommand {
def
minAlternateDepth
(
record
:
VariantContext
,
minAlternateDepth
:
Int
,
minSamplesPass
:
Int
=
1
)
:
Boolean
=
{
record
.
getGenotypes
.
count
(
genotype
=>
{
val
AD
=
if
(
genotype
.
hasAD
)
List
(
genotype
.
getAD
:
_
*
)
else
Nil
if
(
AD
.
nonEmpty
)
AD
.
tail
.
count
(
_
>=
minAlternateDepth
)
>
0
else
true
if
(
AD
.
nonEmpty
&&
minAlternateDepth
>=
0
)
AD
.
tail
.
count
(
_
>=
minAlternateDepth
)
>
0
else
true
})
>=
minSamplesPass
}
...
...
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