From 420725441afd116aa181a18e2e21307aa79f27f1 Mon Sep 17 00:00:00 2001 From: aaron Date: Fri, 11 Dec 2009 16:15:44 +0000 Subject: [PATCH] documentation updates for the new help system. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2323 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/fasta/FastaAlternateReferenceWalker.java | 5 ++++- .../sting/gatk/walkers/fasta/PickSequenomProbes.java | 4 ++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java index 5b8eefa8e..af8d65861 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java @@ -11,7 +11,10 @@ import org.broadinstitute.sting.utils.genotype.Variation; import java.io.*; import java.util.Iterator; - +/** + * Generates an alternative reference sequence over the specified interval. Given a variant ROD track (named "snpmask"), + * it replaces the reference bases at variation sites with the bases supplied by the ROD. + */ @WalkerName("FastaAlternateReferenceMaker") @Requires(value={DataSource.REFERENCE}) public class FastaAlternateReferenceWalker extends FastaReferenceWalker { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java index ed7edb695..8021ce317 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java @@ -11,6 +11,10 @@ import org.broadinstitute.sting.utils.genotype.Variation; import java.util.*; +/** + * Generates Sequenom probe information given a single variant track. Emitted is the variant + * along with the 200 reference bases on each side of the variant. + */ @WalkerName("PickSequenomProbes") @Requires(value={DataSource.REFERENCE}) @Reference(window=@Window(start=-200,stop=200))