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biopet.biopet
Commits
793b521d
Commit
793b521d
authored
Mar 27, 2017
by
Peter van 't Hof
Browse files
Fixed BIOPET-584
parent
2299e7a9
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
View file @
793b521d
...
...
@@ -154,7 +154,10 @@ object VcfWithVcf extends ToolCommand {
* @param header: header of secondary reader
* @return Map of fields and their values in secondary records
*/
def
createFieldMap
(
fields
:
List
[
Fields
],
record
:
VariantContext
,
secondaryRecords
:
List
[
VariantContext
],
header
:
VCFHeader
)
:
Map
[
String
,
List
[
Any
]]
=
{
def
createFieldMap
(
fields
:
List
[
Fields
],
record
:
VariantContext
,
secondaryRecords
:
List
[
VariantContext
],
header
:
VCFHeader
)
:
Map
[
String
,
List
[
Any
]]
=
{
val
fieldMap
=
(
for
(
f
<-
fields
if
secondaryRecords
.
exists
(
_
.
hasAttribute
(
f
.
inputField
))
)
yield
{
...
...
@@ -236,8 +239,8 @@ object VcfWithVcf extends ToolCommand {
* @return
*/
def
numberA
(
referenceRecord
:
VariantContext
,
annotateRecord
:
VariantContext
,
field
:
String
)
:
List
[
Any
]
=
{
val
refValues
=
referenc
eRecord
.
getAttributeAsList
(
field
).
toArray
annotat
eRecord
.
val
refValues
=
annotat
eRecord
.
getAttributeAsList
(
field
).
toArray
referenc
eRecord
.
getAlternateAlleles
.
filter
(
referenceRecord
.
hasAlternateAllele
).
map
(
x
=>
referenceRecord
.
getAlternateAlleles
.
indexOf
(
x
)).
flatMap
(
x
=>
refValues
.
lift
(
x
)).
...
...
@@ -252,8 +255,8 @@ object VcfWithVcf extends ToolCommand {
* @return
*/
def
numberR
(
referenceRecord
:
VariantContext
,
annotateRecord
:
VariantContext
,
field
:
String
)
:
List
[
Any
]
=
{
val
refValues
=
referenc
eRecord
.
getAttributeAsList
(
field
).
toArray
annotat
eRecord
.
val
refValues
=
annotat
eRecord
.
getAttributeAsList
(
field
).
toArray
referenc
eRecord
.
getAlleles
.
filter
(
referenceRecord
.
hasAllele
).
map
(
x
=>
referenceRecord
.
getAlleles
.
indexOf
(
x
)).
...
...
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