Merge pull request #38 from oxfordmmm/fix/nulls-on-filter-fails

Allow multiple filters

VERSION

@@ -1,2 +1 @@
-1.3.5
-
+1.3.6

gumpy/variantfile.py

@@ -80,14 +80,14 @@ def __init__(
 
         # Get the filter attribute value
         assert len(record.filter.items()) >= 0, "A record has more than 1 filter set!"
-        self.filter: str | None
+        self.filter: list[str] | None
         if len(record.filter.items()) == 0:
             self.filter = None
             self.is_filter_pass = False
         else:
-            self.filter = str(record.filter.items()[0][0])
+            self.filter = [str(x) for x in record.filter.keys()]
             self.is_filter_pass = (
-                True if record.filter.items()[0][0] == "PASS" else False
+                True if len(self.filter) == 1 and self.filter == ["PASS"] else False
             )
 
         # Get the info field
@@ -157,8 +157,8 @@ def __init__(
                     self.is_alt = False
                     self.is_reference = False
 
-        if self.is_null:
-            # Override filter fails on nulls to enforce that they are detected
+        if self.is_null and self.filter == ["MIN_FRS"]:
+            # Override MIN_FRS filter fails on nulls to enforce that they are detected
             self.is_filter_pass = True
 
     def __repr__(self) -> str:
@@ -178,7 +178,7 @@ def __repr__(self) -> str:
         if self.filter is None:
             s += ".\t"
         else:
-            s += self.filter + "\t"
+            s += ",".join(self.filter) + "\t"
         for val in self.values.keys():
             if val == "POS":
                 continue
@@ -561,7 +561,7 @@ def __find_calls(self):
                 not record.is_filter_pass
             ):
                 # We only want to allow these through if the filter fail is MIN_FRS
-                if record.filter == "MIN_FRS":
+                if record.filter == ["MIN_FRS"]:
                     # Allow MIN_FRS
                     variant = record.ref
                     variant_type = "ref"

tests/test-cases/TEST-DNA-2.vcf

@@ -10,7 +10,7 @@
 ##contig=<ID=TEST_DNA,length=99>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	03.vcf
 TEST_DNA	2	.	A	G	.	PASS	KMER=15	GT:DP:COV:GT_CONF	./.:2:1,1:2.05
-TEST_DNA	4	.	A	G,T	.	MIN_GT	KMER=15	GT:DP:COV:GT_CONF	./.:4:1,2,2:3.77
+TEST_DNA	4	.	A	G,T	.	MIN_FRS	KMER=15	GT:DP:COV:GT_CONF	./.:4:1,2,2:3.77
 TEST_DNA	6	.	AAA	GGT,GTA,ATA	.	PASS	KMER=15	GT:DP:COV:GT_CONF	./.:4:1,1,1,1:2.76
 TEST_DNA	12	.	C	T	.	PASS	KMER=15	GT:DP:COV:GT_CONF	1/1:50:0,50:200.58
 TEST_DNA	14	.	C	T,G	.	PASS	KMER=15	GT:DP:COV:GT_CONF	2/2:45:0,2,43:155.58

tests/test-cases/TEST-DNA.vcf

@@ -10,7 +10,7 @@
 ##contig=<ID=TEST_DNA,length=99>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	03.vcf
 TEST_DNA	2	.	A	G	.	PASS	KMER=15	GT:DP:COV:GT_CONF	./.:2:1,1:2.05
-TEST_DNA	4	.	A	G,T	.	MIN_GT	KMER=15	GT:DP:COV:GT_CONF	./.:4:1,2,1:3.77
+TEST_DNA	4	.	A	G,T	.	MIN_FRS	KMER=15	GT:DP:COV:GT_CONF	./.:4:1,2,1:3.77
 TEST_DNA	6	.	AAA	GGT,GTA,ATA	.	PASS	KMER=15	GT:DP:COV:GT_CONF	./.:4:1,1,1,1:2.76
 TEST_DNA	12	.	C	T	.	PASS	KMER=15	GT:DP:COV:GT_CONF	1/1:50:0,50:200.58
 TEST_DNA	14	.	C	T,G	.	PASS	KMER=15	GT:DP:COV:GT_CONF	2/2:45:0,2,43:155.58

tests/unit/test_functions.py

@@ -1407,22 +1407,22 @@ def test_vcf_to_df():
             None,
         ],
         "FILTER": [
-            "PASS",
-            "MIN_GT",
-            "PASS",
-            "PASS",
-            "PASS",
-            "PASS",
-            "PASS",
-            "PASS",
-            "PASS",
-            "PASS",
-            "PASS",
-            "PASS",
-            "PASS",
-            "PASS",
-            "PASS",
-            "PASS",
+            ["PASS"],
+            ["MIN_FRS"],
+            ["PASS"],
+            ["PASS"],
+            ["PASS"],
+            ["PASS"],
+            ["PASS"],
+            ["PASS"],
+            ["PASS"],
+            ["PASS"],
+            ["PASS"],
+            ["PASS"],
+            ["PASS"],
+            ["PASS"],
+            ["PASS"],
+            ["PASS"],
         ],
         "INFO": [
             {"KMER": 15},

tests/unit/test_instantiation.py

@@ -2554,9 +2554,9 @@ def test_instanciate_vcf():
 
     for i in range(15):
         if i == 1:
-            assert vcf.records[i].filter == "MIN_GT"
+            assert vcf.records[i].filter == ["MIN_FRS"]
         else:
-            assert vcf.records[i].filter == "PASS"
+            assert vcf.records[i].filter == ["PASS"]
 
     # GT
     gt = [record.values["GT"] for record in vcf.records]