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biopet.biopet
Commits
6bda10a5
Commit
6bda10a5
authored
Jul 24, 2017
by
Peter van 't Hof
Browse files
Skipping double checkChecksum jobs
parent
03beb3f1
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
6bda10a5
...
...
@@ -207,15 +207,18 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
for
(
inputFile
<-
inputFiles
)
{
inputFile
.
md5
match
{
case
Some
(
checksum
)
=>
val
checkMd5
=
new
CheckChecksum
checkMd5
.
inputFile
=
inputFile
.
file
if
(!
SummaryQScript
.
md5sumCache
.
contains
(
inputFile
.
file
))
addChecksum
(
inputFile
.
file
)
checkMd5
.
checksumFile
=
SummaryQScript
.
md5sumCache
(
inputFile
.
file
)
checkMd5
.
checksum
=
checksum
checkMd5
.
jobOutputFile
=
new
File
(
checkMd5
.
checksumFile
.
getParentFile
,
checkMd5
.
checksumFile
.
getName
+
".check.out"
)
add
(
checkMd5
)
if
(!
SummaryQScript
.
checkChecksumCache
.
contains
(
inputFile
.
file
))
{
val
checkMd5
=
new
CheckChecksum
checkMd5
.
inputFile
=
inputFile
.
file
if
(!
SummaryQScript
.
md5sumCache
.
contains
(
inputFile
.
file
))
addChecksum
(
inputFile
.
file
)
checkMd5
.
checksumFile
=
SummaryQScript
.
md5sumCache
(
inputFile
.
file
)
checkMd5
.
checksum
=
checksum
checkMd5
.
jobOutputFile
=
new
File
(
checkMd5
.
checksumFile
.
getParentFile
,
checkMd5
.
checksumFile
.
getName
+
".check.out"
)
add
(
checkMd5
)
SummaryQScript
.
checkChecksumCache
.
add
(
inputFile
.
file
)
}
case
_
=>
}
}
...
...
@@ -238,4 +241,5 @@ object SummaryQScript {
/** Cache to have no duplicate jobs */
protected
[
summary
]
val
md5sumCache
:
mutable.Map
[
File
,
File
]
=
mutable
.
Map
()
protected
[
summary
]
val
checkChecksumCache
:
mutable.Set
[
File
]
=
mutable
.
Set
()
}
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