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quick help/comments updates to match the wikipage. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5569 348d0f76-0448-11de-a6fe-93d51630548a
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carneiro 2011-04-04 12:55:55 +00:00
parent 96f0f0d706
commit b722ebf244
2 changed files with 1 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -85,7 +85,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
@Argument(fullName="select_random_number", shortName="number", doc="Selects a number of variants at random from the variant track. Variants are kept in memory to guarantee that n variants will be output, so use it only for a reasonable number of variants. Use select_random_fraction for larger numbers of variants", required=false)
private int numRandom = 0;
@Argument(fullName="select_random_fraction", shortName="fraction", doc="Selects a fraction (0,1) of variants at random from the variant track. Routine is based on probability, so the final result is not guaranteed to carry the exact fraction. Can be used for large fractions", required=false)
@Argument(fullName="select_random_fraction", shortName="fraction", doc="Selects a fraction (a number between 0 and 1) of the total variants at random from the variant track. Routine is based on probability, so the final result is not guaranteed to carry the exact fraction. Can be used for large fractions", required=false)
private double fractionRandom = 0;

1
scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
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@ -302,7 +302,6 @@ class dataProcessingV2 extends QScript {
//todo -- add scatter gather capability (waiting for khalid's modifications to the queue base
case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
@Output(doc="recalibrated bam index") var recalIndex = new File(outBam + ".bai")
this.input_file :+= inBam
this.recal_file = inRecalFile
this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY