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Fortunately this code isn't used by anyone right now, but it needs to be fixed before someone unwitingly does: flags were wrong according to the SAM spec. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5584 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-04-06 17:16:41 +00:00
parent b231a40da5
commit 1aa4083352
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -192,8 +192,8 @@ public class ReadUtils {
readFlagNames.put(0x8, "MateUnmapped");
readFlagNames.put(0x10, "Forward");
//readFlagNames.put(0x20, "MateForward");
readFlagNames.put(0x4, "FirstOfPair");
readFlagNames.put(0x8, "SecondOfPair");
readFlagNames.put(0x40, "FirstOfPair");
readFlagNames.put(0x80, "SecondOfPair");
readFlagNames.put(0x100, "NotPrimary");
readFlagNames.put(0x200, "NON-PF");
readFlagNames.put(0x400, "Duplicate");