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Fixing a null pointer exception bug for DEV-10

This commit is contained in:
Mauricio Carneiro 2012-10-18 13:58:38 -04:00
parent d3fc797cfe
commit 3504f71b6b
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
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@ -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 )