Merge pull request #209 from ctsa/csi_index

Allow csi-indexed vcf files

Added some changes to it in branch `csidx`. Will need to merge that next since I don't know how to commit directly to a pr.

truvari/__init__.py

@@ -164,6 +164,7 @@
     HEADERMAT,
     LogFileStderr,
     bed_ranges,
+    check_vcf_index,
     cmd_exe,
     compress_index_vcf,
     help_unknown_cmd,

truvari/bench.py

@@ -130,17 +130,15 @@ def check_params(args):
         logging.error("Comparison vcf %s does not end with .gz. Must be bgzip'd",
                       args.comp)
         check_fail = True
-    if not os.path.exists(args.comp + '.tbi'):
-        logging.error("Comparison vcf index %s.tbi does not exist. Must be indexed",
-                      args.comp)
+    if not truvari.check_vcf_index(args.comp):
+        logging.error("Comparison vcf '%s' must be indexed.", args.comp)
         check_fail = True
     if not args.base.endswith(".gz"):
         logging.error("Base vcf %s does not end with .gz. Must be bgzip'd",
                       args.base)
         check_fail = True
-    if not os.path.exists(args.base + '.tbi'):
-        logging.error("Base vcf index %s.tbi does not exist. Must be indexed",
-                      args.base)
+    if not truvari.check_vcf_index(args.base):
+        logging.error("Base vcf '%s' must be indexed.", args.base)
         check_fail = True
     if args.includebed and not os.path.exists(args.includebed):
         logging.error("Include bed %s does not exist", args.includebed)

truvari/phab.py

@@ -459,17 +459,17 @@ def check_params(args):
         logging.error(
             "Comparison vcf %s does not end with .gz. Must be bgzip'd", args.comp)
         check_fail = True
-    if args.comp is not None and not os.path.exists(args.comp + '.tbi'):
+    if args.comp is not None and not truvari.check_vcf_index(args.comp):
         logging.error(
-            "Comparison vcf index %s.tbi does not exist. Must be indexed", args.comp)
+            "Comparison vcf %s must be indexed", args.comp)
         check_fail = True
     if not args.base.endswith(".gz"):
         logging.error(
             "Base vcf %s does not end with .gz. Must be bgzip'd", args.base)
         check_fail = True
-    if not os.path.exists(args.base + '.tbi'):
+    if not truvari.check_vcf_index(args.base):
         logging.error(
-            "Base vcf index %s.tbi does not exist. Must be indexed", args.base)
+            "Base vcf %s must be indexed", args.base)
         check_fail = True
     if not os.path.exists(args.reference):
         logging.error("Reference %s does not exist", args.reference)

truvari/utils.py

@@ -437,3 +437,12 @@ def compress_index_vcf(fn, fout=None, remove=True):
     if remove:
         os.remove(fn)
     os.remove(m_tmp)
+
+
+def check_vcf_index(vcf_path):
+    """
+    Return true if an index file is found for the vcf
+    """
+    vcf_index_ext = ['tbi','csi']
+    return any([os.path.exists(vcf_path + '.' + x) for x in vcf_index_ext])
+