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biopet.biopet
Commits
700bfa35
Commit
700bfa35
authored
10 years ago
by
bow
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Precompile regex for splitting read IDs
parent
20dab674
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+4
-1
4 additions, 1 deletion
.../src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
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4
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View file @
700bfa35
...
...
@@ -90,9 +90,12 @@ class FastqSync(val root: Configurable) extends BiopetJavaCommandLineFunction {
object
FastqSync
extends
ToolCommand
{
/** Regex for capturing read ID ~ taking into account its read pair mark (if present) */
private
val
idRegex
=
"[_/][12]\\s??|\\s"
.
r
/** Implicit class to allow for lazy retrieval of FastqRecord ID without any read pair mark */
private
implicit
class
FastqPair
(
fq
:
FastqRecord
)
{
lazy
val
fragId
=
fq
.
getReadHeader
.
split
(
"[_/][12]\\s??|\\s"
)(
0
)
lazy
val
fragId
=
idRegex
.
split
(
fq
.
getReadHeader
)(
0
)
}
/**
...
...
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