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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
This commit is contained in:
aaron 2010-08-31 17:45:33 +00:00
parent 3d6c4fc55f
commit db4ff7317f
1 changed files with 3 additions and 1 deletions
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4
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -687,7 +687,9 @@ public class GenomeAnalysisEngine {
// compare the tracks to the reference, if they have a sequence dictionary // compare the tracks to the reference, if they have a sequence dictionary
for (RMDTrack track : tracks) { for (RMDTrack track : tracks) {
SAMSequenceDictionary trackDict = track.getSequenceDictionary(); 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"); logger.info("Track " + track.getName() + " doesn't have a sequence dictionary built in, skipping dictionary validation");
continue; continue;
} }