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Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users

This commit is contained in:
Guillermo del Angel 2011-10-11 11:01:06 -04:00
parent 0016c707a3
commit 4c1d8c8d44
2 changed files with 2 additions and 1 deletions
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1
public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
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@ -135,6 +135,7 @@ public class AnalyzeCovariates extends CommandLineProgram {
*/ */
@Argument(fullName="max_histogram_value", shortName="maxHist", required = false, doc="If supplied, this value will be the max value of the histogram plots") @Argument(fullName="max_histogram_value", shortName="maxHist", required = false, doc="If supplied, this value will be the max value of the histogram plots")
private int MAX_HISTOGRAM_VALUE = 0; private int MAX_HISTOGRAM_VALUE = 0;
@Hidden
@Argument(fullName="do_indel_quality", shortName="indels", required = false, doc="If supplied, do indel quality plotting") @Argument(fullName="do_indel_quality", shortName="indels", required = false, doc="If supplied, do indel quality plotting")
private boolean DO_INDEL_QUALITY = false; private boolean DO_INDEL_QUALITY = false;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -63,7 +63,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
private boolean SIMPLE_GREEDY_GENOTYPER = false; private boolean SIMPLE_GREEDY_GENOTYPER = false;
private final static double SUM_GL_THRESH_NOCALL = -0.001; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call. private final static double SUM_GL_THRESH_NOCALL = 0.001; // if max(gl)-min(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call.
final private ExactCalculation calcToUse; final private ExactCalculation calcToUse;
protected ExactAFCalculationModel(UnifiedArgumentCollection UAC, int N, Logger logger, PrintStream verboseWriter) { protected ExactAFCalculationModel(UnifiedArgumentCollection UAC, int N, Logger logger, PrintStream verboseWriter) {