Commit 9cc63752 authored by Peter van 't Hof's avatar Peter van 't Hof

Remove legency code

parent a2c870b2
......@@ -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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