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biopet.biopet
Commits
e5ccc0cf
Commit
e5ccc0cf
authored
Nov 29, 2016
by
Peter van 't Hof
Browse files
Adding refcalls
parent
85708a4a
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
View file @
e5ccc0cf
...
...
@@ -27,7 +27,7 @@ import scala.math.{ floor, round }
object
MpileupToVcf
extends
ToolCommand
{
case
class
Args
(
input
:
File
=
null
,
output
:
File
=
null
,
sample
:
String
=
null
,
minDP
:
Int
=
8
,
minAP
:
Int
=
2
,
homoFraction
:
Double
=
0.8
,
ploidy
:
Int
=
2
,
seqError
:
Double
=
0.005
)
extends
AbstractArgs
homoFraction
:
Double
=
0.8
,
ploidy
:
Int
=
2
,
seqError
:
Double
=
0.005
,
refCalls
:
Boolean
=
false
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
opt
[
File
](
'I'
,
"input"
)
valueName
"<file>"
action
{
(
x
,
c
)
=>
...
...
@@ -54,6 +54,9 @@ object MpileupToVcf extends ToolCommand {
opt
[
Double
](
"seqError"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
seqError
=
x
)
}
opt
[
Unit
](
"refCalls"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
refCalls
=
true
)
}
}
/**
...
...
@@ -172,7 +175,7 @@ object MpileupToVcf extends ToolCommand {
case
_
=>
}
if
(
alt
.
nonEmpty
)
{
if
(
alt
.
nonEmpty
||
commandArgs
.
refCalls
)
{
val
ad
=
for
(
ad
<-
format
(
"AD"
).
toString
.
split
(
","
))
yield
ad
.
toInt
var
left
=
reads
-
dels
val
gt
=
ArrayBuffer
[
Int
]()
...
...
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