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biopet.biopet
Commits
9cc63752
Commit
9cc63752
authored
Mar 20, 2017
by
Peter van 't Hof
Browse files
Remove legency code
parent
a2c870b2
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
9cc63752
...
...
@@ -14,15 +14,15 @@
*/
package
nl.lumc.sasc.biopet.core.summary
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
java.sql.Date
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.extensions.
{
CheckChecksum
,
Md5sum
}
import
nl.lumc.sasc.biopet.core.extensions.
{
CheckChecksum
,
Md5sum
}
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import
org.broadinstitute.gatk.queue.QScript
import
nl.lumc.sasc.biopet.LastCommitHash
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
scala.collection.mutable
import
scala.concurrent.Await
...
...
@@ -185,8 +185,8 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
case
Some
(
checksum
)
=>
{
val
checkMd5
=
new
CheckChecksum
checkMd5
.
inputFile
=
inputFile
.
file
require
(
SummaryQScript
.
md5sumCache
.
contains
(
inputFile
.
file
)
,
s
"Md5 job is not executed, checksum file can't be found for: ${
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"
)
...
...
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