b226cb3af001057dea4635de2d4c6c52f0ebe047
angie
  Sat Jun 20 14:34:08 2020 -0700
New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build.  Updates to other VCF & tree utils.  sorta refs #25278, #25382

diff --git src/hg/utils/otto/nextstrainNcov/sampleCladeLineage.py src/hg/utils/otto/nextstrainNcov/sampleCladeLineage.py
index e3459fa..52ca0e0 100755
--- src/hg/utils/otto/nextstrainNcov/sampleCladeLineage.py
+++ src/hg/utils/otto/nextstrainNcov/sampleCladeLineage.py
@@ -2,27 +2,27 @@
 
 import logging, argparse, sys
 import nextstrainVcf, utils, virusNames
 
 def main():
     parser = argparse.ArgumentParser(description="""
 Read samples and clade assignments from a Nextstrain VCF file.
 Read lineage assignments from lineageFile.  Write out 3 tab-sep columns:
 NS sample ID, clade, lineage.
 """
     )
     parser.add_argument('vcfFile', help='VCF file derived from Nextstrain data')
     parser.add_argument('lineageFile', help='Two-column tab-sep file mapping sample to lineage')
     args = parser.parse_args()
 
-    (vcfSamples, vcfSampleClades) = nextstrainVcf.readVcfSamples(args.vcfFile)
+    (vcfSamples, vcfSampleClades) = nextstrainVcf.readVcfSampleClades(args.vcfFile)
     idLookup = virusNames.makeIdLookup(vcfSamples)
     lineages = utils.dictFromFile(args.lineageFile)
     nsLineages = dict([ (virusNames.maybeLookupSeqName(name, idLookup), lin)
                         for name, lin in lineages.items() ])
     for sample, clade in vcfSampleClades.items():
         lineage = nsLineages.get(sample)
         if (not lineage):
             lineage = ''
         print('\t'.join([sample, clade, lineage]))
 
 main()