From 398dc7a12374f01034f9a2d3896d9777282c3b6f Mon Sep 17 00:00:00 2001 From: Joseph White Date: Mon, 25 May 2015 00:22:31 -0400 Subject: [PATCH] Changed error message for Contigs Out of Order Changed confusing error message for out of order contigs Updated Exception message. --- .../broadinstitute/gatk/utils/SequenceDictionaryUtils.java | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java index 22c7127c2..d0eb0b9f8 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java @@ -165,7 +165,12 @@ public class SequenceDictionaryUtils { } case OUT_OF_ORDER: { - UserException ex = new UserException.IncompatibleSequenceDictionaries("Relative ordering of overlapping contigs differs, which is unsafe", name1, dict1, name2, dict2); + UserException ex = new UserException.IncompatibleSequenceDictionaries( + "The contig order in " + name1 + " and " + name2 + "is not " + + "the same; to fix this please see: " + + "(https://www.broadinstitute.org/gatk/guide/article?id=1328), " + + " which describes reordering contigs in BAM and VCF files.", + name1, dict1, name2, dict2); if ( allowNonFatalIncompabilities(validationExclusion) ) logger.warn(ex.getMessage()); else