475424b5d722b4ff761681f1d3bd91ad666fb2d6
angie
  Wed Apr 1 10:17:03 2020 -0700
For nested clades, add all clade samples to per-clade VCF.  Also generate Newick (.nh) tree file and tweak sample name separator, in preparation for drawing the nextstrain tree in the VCF left label area.  refs #25188

diff --git src/hg/utils/otto/nextstrainNcov/makefile src/hg/utils/otto/nextstrainNcov/makefile
index 40bf27b..f845482 100644
--- src/hg/utils/otto/nextstrainNcov/makefile
+++ src/hg/utils/otto/nextstrainNcov/makefile
@@ -1,6 +1,6 @@
 RUNDIR=/hive/data/outside/otto/nextstrainNcov
 install: 
 	# pylint -E nextstrain.py
 	cp nextstrain.py nextstrainClade.as doUpdate.sh ${RUNDIR}/
 clean:
-	rm -f *.bed *.bb *.gz *.tbi *.json
+	rm -f *.bed *.nh *.vcf *.bb *.gz *.tbi