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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
This commit is contained in:
ebanks 2010-09-15 01:54:50 +00:00
parent 514b28210e
commit dd23f204ab
1 changed files with 3 additions and 0 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -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;