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biopet.biopet
Commits
35dca269
Commit
35dca269
authored
May 11, 2016
by
Peter van 't Hof
Browse files
Added contig check for each record
parent
8fc17a50
Changes
1
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
View file @
35dca269
...
...
@@ -124,6 +124,7 @@ object VcfWithVcf extends ToolCommand {
var
counter
=
0
for
(
record
<-
reader
)
{
require
(
vcfDict
.
getSequence
(
record
.
getContig
)
!=
null
,
s
"Contig ${record.getContig} does not exist on reference"
)
val
secondaryRecords
=
getSecondaryRecords
(
secondaryReader
,
record
,
commandArgs
.
matchAllele
)
val
fieldMap
=
createFieldMap
(
commandArgs
.
fields
,
secondaryRecords
)
...
...
@@ -202,7 +203,6 @@ object VcfWithVcf extends ToolCommand {
}
case
FieldMethod
.
unique
=>
scalaListToJavaObjectArrayList
(
attribute
.
_2
.
distinct
)
case
_
=>
{
print
(
attribute
.
_2
.
getClass
.
toString
)
scalaListToJavaObjectArrayList
(
attribute
.
_2
)
}
})
...
...
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