From cd7a7091babc2f70dba2aa2993bf6e9ac6b23fa3 Mon Sep 17 00:00:00 2001 From: depristo Date: Sat, 19 Feb 2011 23:45:37 +0000 Subject: [PATCH] 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 --- .../broadinstitute/sting/utils/exceptions/UserException.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index b4005f4dd..86e3d479a 100755 --- a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -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))); }