diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java index b575ef6b8..7ee595b21 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java @@ -411,7 +411,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource { */ public SAMReaders(Reads sourceInfo) { for(File readsFile: sourceInfo.getReadsFiles()) { - SAMFileReader2 reader = new SAMFileReader2(readsFile,false); + SAMFileReader2 reader = new SAMFileReader2(readsFile,true); reader.setValidationStringency(sourceInfo.getValidationStringency()); // If no read group is present, hallucinate one.