From db4ff7317fc3a07080aa25437962024fe15fee19 Mon Sep 17 00:00:00 2001 From: aaron Date: Tue, 31 Aug 2010 17:45:33 +0000 Subject: [PATCH] allowing empty RMD files (we need to not validate their sequence dictionaries against the reference in this case) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4173 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 6d7244043..36f6de39c 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -687,7 +687,9 @@ public class GenomeAnalysisEngine { // compare the tracks to the reference, if they have a sequence dictionary for (RMDTrack track : tracks) { SAMSequenceDictionary trackDict = track.getSequenceDictionary(); - if (trackDict == null) { + + // hack: if the sequence dictionary is empty (as well as null which means it doesn't have a dictionary), skip validation + if (trackDict == null || trackDict.size() == 0) { logger.info("Track " + track.getName() + " doesn't have a sequence dictionary built in, skipping dictionary validation"); continue; }