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Temporary hack: force abort with an intelligent message suggesting that users 

specify -B:dbsnp,vcf <filename> if the filename passed if the --DBSNP argument
value contains 'vcf'.  We'll replace this functionality once dbSNP 132 starts
playing nicely with the tagging system.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4749 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-11-29 23:37:30 +00:00
parent 73946716ac
commit abc13d0a90
1 changed files with 4 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
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@ -399,9 +399,12 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
} }
private void initializeConvenienceBindings(AbstractGenomeAnalysisEngine engine, GATKArgumentCollection argCollection) { private void initializeConvenienceBindings(AbstractGenomeAnalysisEngine engine, GATKArgumentCollection argCollection) {
if (argCollection.DBSNPFile != null) if (argCollection.DBSNPFile != null) {
if(argCollection.DBSNPFile.toLowerCase().contains("vcf"))
throw new UserException("--DBSNP (-D) argument currently does not support VCF. To use dbSNP in VCF format, please use -B:dbsnp,vcf <filename>.");
inputs.add(new RMDTriplet(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, "dbsnp", argCollection.DBSNPFile)); inputs.add(new RMDTriplet(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, "dbsnp", argCollection.DBSNPFile));
} }
}
/** /**
* initialize our lists of bindings * initialize our lists of bindings