Fix liftover by making tabix index an option

liftover_restricted_vcf_map.py

@@ -9,7 +9,7 @@
 import copy
 from collections import defaultdict, OrderedDict
 
-def lift_vcfs(vcfs, out_vcf, reference):
+def lift_vcfs(vcfs, out_vcf, reference, tabix_index=True):
   logger = logging.getLogger(lift_vcfs.__name__)
 
   if not vcfs:
@@ -67,10 +67,11 @@ def lift_vcfs(vcfs, out_vcf, reference):
               continue
       vcf_writer.write_record(curr_record)
   vcf_writer.close()
-  pysam.tabix_index(out_vcf, force=True, preset='vcf')
+  if tabix_index:
+      pysam.tabix_index(out_vcf, force=True, preset='vcf')
 
   logger.info("Finished liftover of VCF to original reference")
-  return "{}.gz".format(out_vcf)
+  return "{}.gz".format(out_vcf) if tabix_index else out_vcf
 
 
 def lift_maps(maps, out_map):

varsim.py

@@ -12,6 +12,7 @@
 import glob
 import tempfile
 import re
+import pysam
 from distutils.version import LooseVersion
 from liftover_restricted_vcf_map import lift_vcfs, lift_maps
 from generate_small_test_ref import gen_restricted_ref_and_vcfs 
@@ -402,9 +403,10 @@ def varsim_main(reference,
             makedirs([lifted_dir])
             #quick fix for issue of CN
             convertCN([merged_truth_vcf], "two2one")
-            merged_truth_vcf = lift_vcfs([merged_truth_vcf], os.path.join(lifted_dir, "truth.vcf"), None)
+            merged_truth_vcf = lift_vcfs([merged_truth_vcf], os.path.join(lifted_dir, "truth.vcf"), None, tabix_index=False)
             #quick fix for issue of CN
             convertCN([merged_truth_vcf], "one2two")
+            pysam.tabix_index(merged_truth_vcf, force=True, preset='vcf')
             merged_map = lift_maps([merged_map], os.path.join(lifted_dir, "truth.map"))
 
     if processes: