Bug fix from Michael Ross: mark second read in sequence as second of pair.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1753 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-01 14:34:36 +00:00 · 2009-10-01 14:34:36 +00:00 · 2309d19f6f
parent 48b478f751
commit 2309d19f6f
1 changed files with 1 additions and 1 deletions
--- a/java/src/org/broadinstitute/sting/playground/tools/FastqToBam.java
+++ b/java/src/org/broadinstitute/sting/playground/tools/FastqToBam.java
@ -79,7 +79,7 @@ public class FastqToBam extends CommandLineProgram {
                sr2.setReadPairedFlag(true);
                sr2.setAttribute("RG", READ_GROUP_NAME);
                sr2.setFirstOfPairFlag(false);
-                sr2.setSecondOfPairFlag(false);
+                sr2.setSecondOfPairFlag(true);
                sr2.setMateUnmappedFlag(true);
            }