diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java index 6d4c5fbe2..1ebdac489 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java @@ -48,6 +48,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.bed.BedParser; +import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.vcf.VCFUtils; import javax.activation.*; @@ -85,6 +86,14 @@ public class DeclareValidityWalker extends RodWalker{ public Integer reduceInit() { + for(char a : note.toCharArray()){ + if(Character.isWhitespace(a)) throw new UserException("White space is not allowed in VCF Info fields, please omit it from your build, note, and source arguments."); + } + + for(char b : source.toCharArray()){ + if(Character.isWhitespace(b)) throw new UserException("White space is not allowed in VCF Info fields, please omit it from your build, note, and source arguments."); + } + Set old = VCFUtils.getHeaderFields(getToolkit()); Set newlines = new HashSet(); for(VCFHeaderLine each : old){ @@ -108,6 +117,7 @@ public class DeclareValidityWalker extends RodWalker{ public Map addValidation(int Validity, String Note, String Source){ + HashMap validityAnnots = new HashMap(); validityAnnots.put("validity", Validity); validityAnnots.put("user", System.getenv("USER"));