From 27dfb53d2687fd569fba351de4f8fefb523dc3a6 Mon Sep 17 00:00:00 2001 From: ebanks Date: Sun, 5 Jun 2011 05:18:16 +0000 Subject: [PATCH] We really don't want to be advising the user to use an unsafe option - really, they should fix their busted bam file. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5949 348d0f76-0448-11de-a6fe-93d51630548a --- java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java index c4536d176..f3d9edab9 100755 --- a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java +++ b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java @@ -83,7 +83,7 @@ public class GATKSAMRecord extends SAMRecord { // sanity check that the lengths of the base and quality strings are equal if ( getBaseQualities().length != getReadLength() ) - throw new UserException.MalformedBAM(this, String.format("Error: the number of base qualities does not match the number of bases in %s. Use -DBQ x to set a default base quality score to all reads so GATK can proceed.", mRecord.getReadName())); + throw new UserException.MalformedBAM(this, String.format("Error: the number of base qualities does not match the number of bases in %s.", mRecord.getReadName())); } ///////////////////////////////////////////////////////////////////////////////