diff --git a/java/src/org/broadinstitute/sting/utils/Utils.java b/java/src/org/broadinstitute/sting/utils/Utils.java index ed958131c..179fd3122 100755 --- a/java/src/org/broadinstitute/sting/utils/Utils.java +++ b/java/src/org/broadinstitute/sting/utils/Utils.java @@ -176,6 +176,19 @@ public class Utils { return new String(basesAsbytes); } + public static boolean is454Read(SAMRecord read, SAMFileHeader header) { + Object readGroupAttr = read.getAttribute("RG"); + if ( readGroupAttr != null ) { + SAMReadGroupRecord readGroup = header.getReadGroup(readGroupAttr.toString()); + if ( readGroup != null ) { + Object readPlatformAttr = readGroup.getAttribute("PL"); + if ( readPlatformAttr != null ) + return readPlatformAttr.toString().toUpperCase().contains("454"); + } + } + return false; + } + private static final Map readFlagNames = new HashMap();