From c40efe1deae1847029c6874dd7e853affeae98a7 Mon Sep 17 00:00:00 2001 From: hanna Date: Sun, 6 Mar 2011 13:43:49 +0000 Subject: [PATCH] Fixed exception for BAMs without filenames (unit tests, BAM input streaming, etc.). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5379 348d0f76-0448-11de-a6fe-93d51630548a --- .../broadinstitute/sting/utils/exceptions/UserException.java | 2 +- 1 file changed, 1 insertion(+), 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 f0dc3eeb3..2b21fc473 100755 --- a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -137,7 +137,7 @@ public class UserException extends ReviewedStingException { public static class MalformedBAM extends UserException { public MalformedBAM(SAMRecord read, String message) { - super(String.format("SAM/BAM file %s is malformed: %s", read.getFileSource().getReader(), message)); + super(String.format("SAM/BAM file %s is malformed: %s", read.getFileSource() != null ? read.getFileSource().getReader() : "(none)", message)); } }