LILAC pre v1.6 used to write fragment counts to ref fields in case it was run in tumor-only mode. This has been fixed in LILAC v1.6, and since we depend on that now, we can remove the work-around for this in ORANGE.
With this change, ORANGE assumes tumor fragments are filled in when run in tumor-only mode.
Have tested using COLO829 tumor+ref and tumor-only.
LILAC pre v1.6 used to write fragment counts to ref fields in case it was run in tumor-only mode. This has been fixed in LILAC v1.6, and since we depend on that now, we can remove the work-around for this in ORANGE.
With this change, ORANGE assumes tumor fragments are filled in when run in tumor-only mode.
Have tested using COLO829 tumor+ref and tumor-only.