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one more change needed to commit 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1093 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-25 15:09:53 +00:00
parent f6eeb36c93
commit ea2426dcd0
1 changed files with 13 additions and 0 deletions
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13
java/src/org/broadinstitute/sting/utils/Utils.java
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@ -176,6 +176,19 @@ public class Utils {
return new String(basesAsbytes); 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<Integer, String> readFlagNames private static final Map<Integer, String> readFlagNames
= new HashMap<Integer, String>(); = new HashMap<Integer, String>();