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Added option of minMappingQuality 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6002 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2011-06-16 00:02:26 +00:00
parent ce4e8d2093
commit b4c30bf124
1 changed files with 4 additions and 1 deletions
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5
scala/qscript/oneoffs/fromer/CNV/ReadDepthCNVanalysis.scala
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@ -40,6 +40,9 @@ class ReadDepthCNVanalysis extends QScript {
@Input(doc = "Starting value of read-depth bins", shortName = "START_BIN", required = false) @Input(doc = "Starting value of read-depth bins", shortName = "START_BIN", required = false)
var START_BIN = 1 var START_BIN = 1
@Input(doc = "Minimum read mapping quality", shortName = "MMQ", required = false)
var minMappingQuality = 0
val DOC_OUTPUT_SUFFIX: String = ".sample_interval_summary" val DOC_OUTPUT_SUFFIX: String = ".sample_interval_summary"
val DOC_MEAN_COVERAGE_OUTPUT: String = ".sample_interval.averageCoverage.txt" val DOC_MEAN_COVERAGE_OUTPUT: String = ".sample_interval.averageCoverage.txt"
@ -109,7 +112,7 @@ class ReadDepthCNVanalysis extends QScript {
var intervalSampleOut: File = new File(t.DoC_output.getPath() + DOC_OUTPUT_SUFFIX) var intervalSampleOut: File = new File(t.DoC_output.getPath() + DOC_OUTPUT_SUFFIX)
override def commandLine = super.commandLine + override def commandLine = super.commandLine +
" --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 0" + " --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality " + minMappingQuality +
" --start " + START_BIN + " --stop " + MAX_DEPTH + " --nBins " + NUM_BINS + " --start " + START_BIN + " --stop " + MAX_DEPTH + " --nBins " + NUM_BINS +
" -o " + new File(intervalSampleOut.getParentFile(), t.DoC_output.getName()) " -o " + new File(intervalSampleOut.getParentFile(), t.DoC_output.getName())