From 3504f71b6b6be2ac7b97a5886c3609ca4c2caee6 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Thu, 18 Oct 2012 13:58:38 -0400 Subject: [PATCH] Fixing a null pointer exception bug for DEV-10 --- .../gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java index 2ea4bdfb0..00c6ddae8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java @@ -123,13 +123,13 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor // This parser has been passed a null filename and the GATK is not responsible for creating a type default for the object; // therefore, the user must have failed to specify a type default - if(writerFileName.asFile() == null && generateMD5) + if(writerFileName != null && writerFileName.asFile() == null && generateMD5) throw new ArgumentException("MD5 generation specified, but no output file specified. If md5 generation is desired, please specify a BAM output file and an md5 file will be written alongside."); // Create the stub and set parameters. SAMFileWriterStub stub = null; // stub = new SAMFileWriterStub(engine, defaultOutputStream); - if ( writerFileName.asFile() != null ) { + if (writerFileName != null && writerFileName.asFile() != null ) { stub = new SAMFileWriterStub(engine, writerFileName.asFile()); if ( compressionLevel != null )