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biopet.biopet
Commits
43006ba6
Commit
43006ba6
authored
May 25, 2016
by
Peter van 't Hof
Browse files
Filter references calls
parent
afb31099
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
43006ba6
...
...
@@ -148,7 +148,7 @@ object VcfFilter extends ToolCommand {
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
logger
.
info
(
"Start"
)
val
argsParser
=
new
OptParser
val
cmdArgs
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
cmdArgs
=
argsParser
.
parse
(
args
,
Args
())
.
getOrElse
{
throw
new
IllegalArgumentException
}
val
reader
=
new
VCFFileReader
(
cmdArgs
.
inputVcf
,
false
)
val
header
=
reader
.
getFileHeader
...
...
@@ -226,7 +226,9 @@ object VcfFilter extends ToolCommand {
* @return false when filter fails
*/
def
hasGenotype
(
record
:
VariantContext
,
samplesGenotypes
:
List
[(
String
,
GenotypeType
)])
:
Boolean
=
{
samplesGenotypes
.
forall
(
x
=>
record
.
getGenotype
(
x
.
_1
).
getType
==
x
.
_2
)
samplesGenotypes
.
forall
{
x
=>
record
.
getGenotype
(
x
.
_1
).
getType
==
x
.
_2
}
}
/**
...
...
@@ -346,6 +348,7 @@ object VcfFilter extends ToolCommand {
if
(
sample
==
null
)
return
true
val
genotype
=
record
.
getGenotype
(
sample
)
if
(
genotype
.
isNoCall
)
return
false
if
(
genotype
.
getAlleles
.
forall
(
_
.
isReference
))
return
false
for
(
allele
<-
genotype
.
getAlleles
if
allele
.
isNonReference
)
{
for
(
g
<-
record
.
getGenotypes
if
g
.
getSampleName
!=
sample
)
{
if
(
g
.
getAlleles
.
exists
(
_
.
basesMatch
(
allele
)))
return
false
...
...
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