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biopet.biopet
Commits
90ad4035
Commit
90ad4035
authored
Oct 04, 2016
by
Sander Bollen
Browse files
better way of finding these types of variants
parent
af617116
Changes
2
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
90ad4035
...
...
@@ -16,10 +16,10 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
htsjdk.variant.variantcontext.
{
GenotypeType
,
VariantContext
}
import
htsjdk.variant.variantcontext.writer.
{
AsyncVariantContextWriter
,
VariantContextWriterBuilder
}
import
htsjdk.variant.variantcontext.
{
GenotypeType
,
VariantContext
}
import
htsjdk.variant.variantcontext.writer.
{
AsyncVariantContextWriter
,
VariantContextWriterBuilder
}
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.utils.
{
ToolCommand
,
VcfUtils
}
import
nl.lumc.sasc.biopet.utils.
{
ToolCommand
,
VcfUtils
}
import
scala.collection.JavaConversions._
import
scala.io.Source
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
View file @
90ad4035
...
...
@@ -142,11 +142,11 @@ object VcfUtils {
}
/**
* Check whether genotype is of the from 0/.
* @param genotype genotype
* @return boolean
*/
* Check whether genotype is of the from 0/.
* @param genotype genotype
* @return boolean
*/
def
isCompoundNoCall
(
genotype
:
Genotype
)
:
Boolean
=
{
!
genotype
.
is
HetNonRef
&&
genotype
.
isMix
ed
&&
genotype
.
getAlleles
.
last
.
basesMatch
(
""
)
genotype
.
is
Call
ed
&&
genotype
.
getAlleles
.
exists
(
_
.
isNoCall
)
}
}
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