Add more error types for unsupported features

Author: tomwhite

tests/test_filter.py

@@ -35,8 +35,9 @@ def test_invalid_expressions(self, parser, expression):
             # generic string issue. Can fix this later when we've gotten
             # some partial string handling implemented
             ("INFO/HAYSTACK ~ 0", filter_mod.UnsupportedRegexError),
-            ('CHROM="1"', filter_mod.UnsupportedStringsError),
-            ('FILTER="PASS"', filter_mod.UnsupportedStringsError),
+            ('CHROM="1"', filter_mod.UnsupportedChromFieldError),
+            ('DP="."', filter_mod.UnsupportedMissingDataError),
+            ('FILTER="PASS"', filter_mod.UnsupportedFilterFieldError),
             ("ID!=@~/file", filter_mod.UnsupportedFileReferenceError),
             ("INFO/TAG=@file", filter_mod.UnsupportedFileReferenceError),
             ("INFO/X[0] == 1", filter_mod.UnsupportedArraySubscriptError),

vcztools/filter.py

@@ -27,26 +27,46 @@ def __init__(self):
         )
 
 
-class UnsupportedRegexError(UnsupportedFilteringFeatureError):
-    issue = "174"
-    feature = "Regular expressions"
+class UnsupportedMissingDataError(UnsupportedFilteringFeatureError):
+    issue = "163"
+    feature = "Missing data"
+
+
+class UnsupportedFilterFieldError(UnsupportedFilteringFeatureError):
+    issue = "164"
+    feature = "FILTER field"
+
+
+class UnsupportedGenotypeValuesError(UnsupportedFilteringFeatureError):
+    issue = "165"
+    feature = "Genotype values"
 
 
 class UnsupportedArraySubscriptError(UnsupportedFilteringFeatureError):
     issue = "167"
     feature = "Array subscripts"
 
 
-class UnsupportedStringsError(UnsupportedFilteringFeatureError):
-    issue = "189"
-    feature = "String values temporarily removed"
+class UnsupportedRegexError(UnsupportedFilteringFeatureError):
+    issue = "174"
+    feature = "Regular expressions"
 
 
 class UnsupportedFileReferenceError(UnsupportedFilteringFeatureError):
     issue = "175"
     feature = "File references"
 
 
+class UnsupportedChromFieldError(UnsupportedFilteringFeatureError):
+    issue = "178"
+    feature = "CHROM field"
+
+
+class UnsupportedStringsError(UnsupportedFilteringFeatureError):
+    issue = "189"
+    feature = "String values temporarily removed"
+
+
 class UnsupportedFunctionsError(UnsupportedFilteringFeatureError):
     issue = "190"
     feature = "Function evaluation"
@@ -89,7 +109,11 @@ class Number(Constant):
 
 class String(Constant):
     def __init__(self, tokens):
-        raise UnsupportedStringsError()
+        super().__init__(tokens)
+        if self.tokens == ".":
+            raise UnsupportedMissingDataError()
+        else:
+            raise UnsupportedStringsError()
 
 
 class FileReference(Constant):
@@ -104,8 +128,15 @@ def __init__(self, tokens):
 
 class Identifier(EvaluationNode):
     def __init__(self, mapper, tokens):
-        self.field_name = mapper(tokens[0])
-        logger.debug(f"Mapped {tokens[0]} to {self.field_name}")
+        token = tokens[0]
+        if token == "CHROM":
+            raise UnsupportedChromFieldError()
+        elif token == "FILTER":
+            raise UnsupportedFilterFieldError()
+        elif token == "GT":
+            raise UnsupportedGenotypeValuesError()
+        self.field_name = mapper(token)
+        logger.debug(f"Mapped {token} to {self.field_name}")
 
     def eval(self, data):
         value = np.asarray(data[self.field_name])