diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReadStreamResource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReadStreamResource.java index ce91d3a99..1eee99679 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReadStreamResource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReadStreamResource.java @@ -45,6 +45,8 @@ import java.io.File; * @version 0.1 */ class ReadStreamResource { + final static boolean eagerDecode = true; + /** our log, which we want to capture anything from this class */ protected static Logger logger = Logger.getLogger(ReadStreamPointer.class); @@ -124,7 +126,7 @@ class ReadStreamResource { // right now this is pretty damn heavy, it copies the file list into a reader list every time List lst = new ArrayList(); for (File f : reads.getReadsFiles()) { - SAMFileReader reader = new SAMFileReader(f, true); + SAMFileReader reader = new SAMFileReader(f, eagerDecode); reader.setValidationStringency(reads.getValidationStringency()); final SAMFileHeader header = reader.getFileHeader();