Short:
Removed duplicate code fragment that had no effect.
Long:
When adding a new read pair to a SAMRecord using the addPair() method in SAMRecordSetBuilder,
the parameters "record1NonPrimary" as well as "record2NonPrimary" are checked to set the
secondary alignment flag of the SAM record. This code fragment for both reads was duplicated with
no effect. The duplicate is removed in this PR.
…eadpair
Description
Short: Removed duplicate code fragment that had no effect.
Long: When adding a new read pair to a SAMRecord using the addPair() method in SAMRecordSetBuilder, the parameters "record1NonPrimary" as well as "record2NonPrimary" are checked to set the secondary alignment flag of the SAM record. This code fragment for both reads was duplicated with no effect. The duplicate is removed in this PR.