From 6e69193e3c4f018dd061a8b9e94ccd01fa1c2087 Mon Sep 17 00:00:00 2001 From: aaron Date: Tue, 12 May 2009 18:52:42 +0000 Subject: [PATCH] Deprecated calls to getSamReader on both the GenomeAnalysisEngine and the TraversalEngine. This call fails in the new style traversals, but it won't disapear until the cut-over to the new traversals is complete. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@671 348d0f76-0448-11de-a6fe-93d51630548a --- .../broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 8 +++++++- .../sting/gatk/traversals/TraversalEngine.java | 2 +- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 7659c8a9e..2710aad25 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -293,7 +293,13 @@ public class GenomeAnalysisEngine { return outputTracker; } - + /** + * This function is deprecated in the new traversal engines, if you need to get the header + * please get the engine and then use the getHeader function + * + * @return + */ + @Deprecated public SAMFileReader getSamReader() { return this.engine.getSamReader(); } diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java index 5d92c5c2d..85ca68f13 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java @@ -590,6 +590,6 @@ public abstract class TraversalEngine { logger.warn(msg); } } - + @Deprecated public SAMFileReader getSamReader() { return this.samReader; } }