From 4c1d8c8d44100735c0c310977d5e22d3223740fa Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Tue, 11 Oct 2011 11:01:06 -0400 Subject: [PATCH 1/3] Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users --- .../sting/analyzecovariates/AnalyzeCovariates.java | 1 + .../sting/gatk/walkers/genotyper/ExactAFCalculationModel.java | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java index 1ef452a5c..548678ddb 100755 --- a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java +++ b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java @@ -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") private int MAX_HISTOGRAM_VALUE = 0; + @Hidden @Argument(fullName="do_indel_quality", shortName="indels", required = false, doc="If supplied, do indel quality plotting") private boolean DO_INDEL_QUALITY = false; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java index 6ae437b27..62912d375 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java @@ -63,7 +63,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel { 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; protected ExactAFCalculationModel(UnifiedArgumentCollection UAC, int N, Logger logger, PrintStream verboseWriter) { From 6506ea83e8f348a39a62cba9387a618dd6b4deb2 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Tue, 11 Oct 2011 11:03:12 -0400 Subject: [PATCH 2/3] Revert "Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users"... a hidden passenger change made it through. This reverts commit 70e10ccb1be90dcff8f4485ae6ee036db2d1ac86. --- .../sting/analyzecovariates/AnalyzeCovariates.java | 1 - .../sting/gatk/walkers/genotyper/ExactAFCalculationModel.java | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java index 548678ddb..1ef452a5c 100755 --- a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java +++ b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java @@ -135,7 +135,6 @@ 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") private int MAX_HISTOGRAM_VALUE = 0; - @Hidden @Argument(fullName="do_indel_quality", shortName="indels", required = false, doc="If supplied, do indel quality plotting") private boolean DO_INDEL_QUALITY = false; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java index 62912d375..6ae437b27 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java @@ -63,7 +63,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel { private boolean SIMPLE_GREEDY_GENOTYPER = false; - 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. + 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. final private ExactCalculation calcToUse; protected ExactAFCalculationModel(UnifiedArgumentCollection UAC, int N, Logger logger, PrintStream verboseWriter) { From 1975de1b3220f9827e938b010141f7d32a72de7b Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Tue, 11 Oct 2011 11:11:29 -0400 Subject: [PATCH 3/3] Second try: hide --do_indel_quality in AnalyzeCovariates --- .../sting/analyzecovariates/AnalyzeCovariates.java | 1 + 1 file changed, 1 insertion(+) diff --git a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java index 1ef452a5c..548678ddb 100755 --- a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java +++ b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java @@ -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") private int MAX_HISTOGRAM_VALUE = 0; + @Hidden @Argument(fullName="do_indel_quality", shortName="indels", required = false, doc="If supplied, do indel quality plotting") private boolean DO_INDEL_QUALITY = false;