From dd23f204ab4ce284976a8f440ed2d547a845ff84 Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 15 Sep 2010 01:54:50 +0000 Subject: [PATCH] Making the UG args that allow users to proceed with insufficient bam headers (no SM or PL tags) @Hidden; removed them from wiki. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4283 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 36d0362de..e82a34caf 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Hidden; public class UnifiedArgumentCollection { @@ -64,9 +65,11 @@ public class UnifiedArgumentCollection { // control the error modes + @Hidden @Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false) public String ASSUME_SINGLE_SAMPLE = null; + @Hidden @Argument(fullName = "platform", shortName = "pl", doc = "Causes the genotyper to assume that reads without PL header TAG are this platform. Defaults to null, indicating that the system will throw a runtime exception when such reads are detected", required = false) public EmpiricalSubstitutionProbabilities.SequencerPlatform defaultPlatform = null;