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Fixed fragment handling in DepthOfCoverage

This commit is contained in:
Menachem Fromer 2012-11-21 16:01:10 -05:00
parent 06261b58c2
commit a8c7edca05
1 changed files with 1 additions and 6 deletions
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7
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/CNV/xhmmCNVpipeline.scala
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@ -45,12 +45,7 @@ class xhmmCNVpipeline extends QScript {
@Hidden @Hidden
@Argument(doc = "How should overlapping reads from the same fragment be handled?", shortName = "countType", required = false) @Argument(doc = "How should overlapping reads from the same fragment be handled?", shortName = "countType", required = false)
// TODO: change this to be the default once reads can be ordered properly for FragmentUtils.create(): var countType = CoverageUtils.CountPileupType.COUNT_FRAGMENTS
//
// Don't want to double-count (but also don't mind counting base-inconsistencies in overlap):
//var countType = CoverageUtils.CountPileupType.COUNT_FRAGMENTS
//
var countType = CoverageUtils.CountPileupType.COUNT_READS
@Argument(doc = "Maximum depth (before GATK down-sampling kicks in...)", shortName = "MAX_DEPTH", required = false) @Argument(doc = "Maximum depth (before GATK down-sampling kicks in...)", shortName = "MAX_DEPTH", required = false)
var MAX_DEPTH = 20000 var MAX_DEPTH = 20000