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The -rf argument is now being used for read filter and is colliding with my walkers. Changed mine to -recalFile 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2048 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2009-11-14 19:37:46 +00:00
parent b05119987c
commit 88fd762436
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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@ -72,7 +72,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
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 = 3;
@Argument(fullName="recal_file", shortName="rf", required=false, doc="Filename for the outputted covariates table recalibration file")
@Argument(fullName="recal_file", shortName="recalFile", 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")
private boolean NO_PRINT_HEADER = false;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/TableRecalibrationWalker.java
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@ -56,7 +56,7 @@ import java.io.FileNotFoundException;
@WalkerName("TableRecalibrationRefactored")
public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
@Argument(fullName="recal_file", shortName="rf", doc="Input recalibration table file generated by CountCovariates", required=true)
@Argument(fullName="recal_file", shortName="recalFile", doc="Input recalibration table file generated by CountCovariates", required=true)
public String RECAL_FILE;
@Argument(fullName="outputBam", shortName="outputBam", doc="output BAM file", required=false)
public SAMFileWriter OUTPUT_BAM = null;