From 5a0a9bc488d8ede546967eccb1788b27c60901d2 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Tue, 19 Feb 2013 10:18:35 -0500 Subject: [PATCH] Hide arguments related to reference sample operation in UG - for internal use only until paper is published and docs are polished. --- .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index a7f90ebec..14d827747 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -150,6 +150,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection Generalized ploidy argument (debug only): When building site error models, ignore lane information and build only sample-level error model */ + @Hidden @Argument(fullName = "ignoreLaneInfo", shortName = "ignoreLane", doc = "Ignore lane when building error model, error model is then per-site", required = false) public boolean IGNORE_LANE_INFO = false; @@ -157,6 +158,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection Generalized ploidy argument: VCF file that contains truth calls for reference sample. If a reference sample is included through argument -refsample, then this argument is required. */ + @Hidden @Input(fullName="reference_sample_calls", shortName = "referenceCalls", doc="VCF file with the truth callset for the reference sample", required=false) RodBinding referenceSampleRod; @@ -165,6 +167,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection that a bar-coded reference sample be included with the polyploid/pooled data in a sequencing experimental design. If argument is absent, no per-site error model is included and calling is done with a generalization of traditional statistical calling. */ + @Hidden @Argument(shortName="refsample", fullName="reference_sample_name", doc="Reference sample name.", required=false) String referenceSampleName; @@ -174,6 +177,10 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection @Argument(shortName="ploidy", fullName="sample_ploidy", doc="Plody (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).", required=false) public int samplePloidy = GATKVariantContextUtils.DEFAULT_PLOIDY; + + /** + * The following argument are for debug-only tweaks when running generalized ploidy with a reference sample + */ @Hidden @Argument(shortName="minqs", fullName="min_quality_score", doc="Min quality score to consider. Smaller numbers process faster. Default: Q1.", required=false) byte minQualityScore= 1;