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oops, putting the script back into a sensible state 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5765 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-05-04 20:17:05 +00:00
parent b5ab2274f6
commit 825682f58c
1 changed files with 1 additions and 7 deletions
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8
scala/qscript/oneoffs/rpoplin/Phase1ProjectConsensus.scala
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@ -65,7 +65,7 @@ class Phase1ProjectConsensus extends QScript {
def script = {
for(chr <- List(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23)) {
for(chr <- List(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23)) {
val chrObject = new Chromosome(chr)
val basesPerJob: Int = 3000000
val lastBase: Int = qscript.chromosomeLength(chr - 1)
@ -142,12 +142,6 @@ class Phase1ProjectConsensus extends QScript {
clean.targetIntervals = targetIntervals
clean.out = cleanedBam
clean.doNotUseSW = true
clean.maxInMemory = 8000
clean.maxReads = 100
clean.greedy = 80
clean.LOD = 7.0
clean.knownsOnly = true
clean.maxConsensuses = 10
clean.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF
clean.simplifyBAM = true
clean.rodBind :+= RodBind("indels1", "VCF", qscript.dindelCalls)