Revert last change. Downsampling does have a positive impact on memory

consumption but produces a lossy BAM, which is not acceptable.
hartwigmedical · Feb 17, 2019 · 6290299 · 6290299
1 parent c4e071a
commit 6290299
Show file tree

Hide file tree

Showing 2 changed files with 0 additions and 2 deletions.
diff --git a/QScripts/BaseRecalibration.scala b/QScripts/BaseRecalibration.scala
@@ -44,7 +44,6 @@ class BaseRecalibration extends QScript {
 
     baseRecalibrator.scatterCount = numScatters
     baseRecalibrator.nct = numCPUThreads
-    baseRecalibrator.dcov = 25000
 
     // KODU: Apply the recalibration to the sequence data
     printReads.input_file :+= bamFile

diff --git a/QScripts/IndelRealignment.scala b/QScripts/IndelRealignment.scala
@@ -48,7 +48,6 @@ class IndelRealignment extends QScript {
 				indelRealigner.targetIntervals = targetCreator.out
 				indelRealigner.input_file +:= bamFile
 				indelRealigner.scatterCount = numScatters
-        indelRealigner.dcov = 25000
 
 				indelRealigner.out = swapExt(bamFile, "bam", "realigned.bam")