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Merge pull request #1001 from broadinstitute/jw_clarify_overlaping_contigs 

Changed error message for Contigs Out of Order
This commit is contained in:
Geraldine Van der Auwera 2015-06-12 15:03:10 -04:00
parent 2a7f95eddb 398dc7a123
commit 456fefa860
1 changed files with 6 additions and 1 deletions
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7
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java
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@ -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