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biopet.biopet
Commits
3b3dc0f4
Commit
3b3dc0f4
authored
May 09, 2015
by
Peter van 't Hof
Browse files
Added catch for U to T
parent
07c86968
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
View file @
3b3dc0f4
...
...
@@ -154,6 +154,7 @@ object MpileupToVcf extends ToolCommand {
val
ref
=
values
(
2
)
match
{
case
"A"
|
"T"
|
"G"
|
"C"
=>
values
(
2
)
case
"a"
|
"t"
|
"g"
|
"c"
=>
values
(
2
).
toUpperCase
case
"U"
|
"u"
=>
"T"
case
_
=>
"N"
}
val
reads
=
values
(
3
).
toInt
...
...
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