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biopet.biopet
Commits
f5f2787f
Commit
f5f2787f
authored
Mar 31, 2016
by
Peter van 't Hof
Browse files
Fixed bug in vcffilter
parent
3cc33596
Changes
1
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public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
f5f2787f
...
...
@@ -276,8 +276,10 @@ object VcfFilter extends ToolCommand {
* @return
*/
def
minGenomeQuality
(
record
:
VariantContext
,
minGQ
:
Int
,
minSamplesPass
:
Int
=
1
)
:
Boolean
=
{
record
.
getGenotypes
.
count
(
x
=>
if
(!
x
.
hasGQ
)
false
else
if
(
x
.
getGQ
>=
minGQ
)
true
else
false
)
>=
minSamplesPass
record
.
getGenotypes
.
count
(
x
=>
if
(
minGQ
==
0
)
true
else
if
(!
x
.
hasGQ
)
false
else
if
(
x
.
getGQ
>=
minGQ
)
true
else
false
)
>=
minSamplesPass
}
/**
...
...
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