diff --git a/bin/passim.cmd b/bin/passim.cmd
index 3769854..c6bbfa3 100644
--- a/bin/passim.cmd
+++ b/bin/passim.cmd
@@ -1,3 +1,29 @@
 @echo off
-call %~dp0seriatim --all-pairs ^
-  --fields "xxhash64(series)^ as^ gid" -f gid^<gid2 %*
\ No newline at end of file
+
+:: Replace special characters <, >, |, & in all arguments with a placeholder
+:: which will be replaced with the original character in seriatim.py
+:: NB: unfortunately, this does not work with the equals sign; use _EQ_, _LTE_ and _GTE_ instead.
+
+:: make sure variables are not expanded before the script is run:
+SETLOCAL EnableDelayedExpansion
+
+:: first, set up an empty variable that will contain all modified variables:
+set modifiedArgs=
+
+:: loop through all arguments passed to the script (%*)
+:: and replace all special characters in them
+:: finally, add each argument to the modified arguments list
+for %%i in (%*) do (
+  set arg=%%i
+  set arg=!arg:^<=_LT_!
+  set arg=!arg:^>=_GT_!
+  set arg=!arg:^|=_PIPE_!
+  set arg=!arg:^&=_AMPERSAND_!
+  set modifiedArgs=!modifiedArgs! !arg!
+  echo !arg!
+)
+::echo MODIFIED ARGS:
+::echo %modifiedArgs%
+
+echo %~dp0seriatim.cmd --all-pairs --fields "xxhash64(series) as gid" -f gid_LT_gid2 %modifiedArgs%
+call %~dp0seriatim.cmd --all-pairs --fields "xxhash64(series) as gid" -f gid_LT_gid2 %modifiedArgs%
diff --git a/passim/seriatim.py b/passim/seriatim.py
index a5ca6ad..3780089 100644
--- a/passim/seriatim.py
+++ b/passim/seriatim.py
@@ -545,6 +545,12 @@ def clusterJoin(self, config, corpus):
 
 setattr(DataFrame, 'clusterJoin', clusterJoin)
 
+def replace_placeholders(s):
+  try:
+    return s.replace("_LT_", "<").replace("_LTE_", "<=").replace("_GT_", ">").replace("_GTE_", ">=").replace("_PIPE_", "|").replace("_AMPERSAND_", "&")
+  except:
+    return s
+
 def main(args):
     parser = argparse.ArgumentParser(description='Passim Alignment',
                                      formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -597,6 +603,9 @@ def main(args):
     parser.add_argument('outputPath', metavar='<path>', help='output')
     config = parser.parse_args(args)
 
+    # replace placeholders in the relevant arguments:
+    config.filterpairs = replace_placeholders(config.filterpairs)
+    config.link_features = replace_placeholders(config.link_features)
     print(config)
 
     spark = SparkSession.builder.appName('Passim Alignment').getOrCreate()