From be902375aceb6cd6f70943b8a20609ff2d2c746a Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 29 Oct 2012 16:29:27 -0400 Subject: [PATCH] 'Bug' fix: fix the error message from the vcf validator so people realize that the file fails strict validation but still adheres to the spec. --- .../sting/gatk/walkers/variantutils/ValidateVariants.java | 2 +- .../sting/utils/exceptions/UserException.java | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java index c92551a73..2f4d24312 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java @@ -172,7 +172,7 @@ public class ValidateVariants extends RodWalker { numErrors++; logger.warn("***** " + e.getMessage() + " *****"); } else { - throw new UserException.MalformedFile(file, e.getMessage()); + throw new UserException.FailsStrictValidation(file, e.getMessage()); } } } diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index c1f408bc7..a49a12292 100755 --- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -283,6 +283,12 @@ public class UserException extends ReviewedStingException { } } + public static class FailsStrictValidation extends UserException { + public FailsStrictValidation(File f, String message) { + super(String.format("File %s fails strict validation: %s", f.getAbsolutePath(), message)); + } + } + public static class MalformedFile extends UserException { public MalformedFile(String message) { super(String.format("Unknown file is malformed: %s", message));