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Default window size for NQS covariate is 3 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2040 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin 2009-11-13 19:24:27 +00:00
parent 394c839974
commit d1b525b428
2 changed files with 2 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java
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@ -71,7 +71,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
@Argument(fullName = "platform", shortName="pl", doc="Which sequencing technology was used? This is important for the cycle covariate. Options are SLX, 454, and SOLID.", required=false)
private String PLATFORM = "SLX";
@Argument(fullName = "windowSizeNQS", shortName="nqs", doc="How big of a window should the MinimumNQSCovariate use for its calculation", required=false)
private int WINDOW_SIZE = 1;
private int WINDOW_SIZE = 3;
@Argument(fullName="recal_file", shortName="rf", required=false, doc="Filename for the outputted covariates table recalibration file")
private String RECAL_FILE = "output.recal_data.csv";
@Argument(fullName="noPrintHeader", shortName="noHeader", required=false, doc="Don't print the usual header on the table recalibration file")

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/TableRecalibrationWalker.java
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@ -67,7 +67,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
@Argument(fullName = "platform", shortName="pl", doc="Which sequencing technology was used? This is important for the cycle covariate. Options are SLX, 454, and SOLID.", required=false)
private String PLATFORM = "SLX";
@Argument(fullName = "windowSizeNQS", shortName="nqs", doc="How big of a window should the MinimumNQSCovariate use for its calculation", required=false)
private int WINDOW_SIZE = 1;
private int WINDOW_SIZE = 3;
@Argument(fullName="smoothing", shortName="sm", required = false, doc="Number of imaginary counts to add to each bin in order to smooth out bins with few data points")
public int SMOOTHING = 1;