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Lexicographic error points users to the ReorderSam wiki entry 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5281 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2011-02-19 23:45:37 +00:00
parent 7323b05dc1
commit cd7a7091ba
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
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@ -199,7 +199,8 @@ public class UserException extends ReviewedStingException {
public LexicographicallySortedSequenceDictionary(String name, SAMSequenceDictionary dict) {
super(String.format("Lexicographically sorted human genome sequence detected in %s."
+ "\nFor safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs."
+ "\nThis is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files"
+ "\nThis is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files."
+ "\nYou can use the ReorderSam utility to fix this problem: http://www.broadinstitute.org/gsa/wiki/index.php/ReorderSam"
+ "\n %s contigs = %s",
name, name, prettyPrintSequenceRecords(dict)));
}