partial fix for #217

CHANGES.md

@@ -1,3 +1,6 @@
+# v0.30.10
++ fix is_indel for <NON_REF> (see #217)
+
 # 0.3.8
 + just bumping for CI+wheels
 

cyvcf2/__init__.py

@@ -2,4 +2,4 @@
                      par_het)
 Reader = VCFReader = VCF
 
-__version__ = "0.30.9"
+__version__ = "0.30.10"

cyvcf2/cyvcf2.pyx

@@ -1830,18 +1830,18 @@ cdef class Variant(object):
         "boolean indicating if the variant is an indel."
         def __get__(self):
             cdef int i
-            is_sv = self.is_sv
-            if len(self.b.d.allele[0]) > 1 and not is_sv: return True
+            if self.is_sv: return False
+            if len(self.b.d.allele[0]) > 1 and self.b.d.allele[0] != '<': return True
 
-            if len(self.REF) > 1 and not is_sv: return True
+            if len(self.REF) > 1: return True
 
             for i in range(1, self.b.n_allele):
                 alt = self.b.d.allele[i]
+                if alt[0] == '<': continue
                 if alt == b".":
                     return True
-                if len(alt) != len(self.REF):
-                    if not is_sv:
-                        return True
+                if len(alt) > 1:
+                    return True
             return False
 
     property is_transition:

cyvcf2/tests/test.isa.vcf

@@ -0,0 +1,10 @@
+##fileformat=VCFv4.2
+##fileDate=20200122
+##contig=<ID=chr1,length=1348724>
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+chr1	146999	.	TCGGT	<NON_REF>	0	.	AC=0
+chr1	146999	.	TCGGT	TGGGG	0	.	AC=0
+chr1	146999	.	T	TG	0	.	AC=0
+chr1	146999	.	TG	T	0	.	AC=0
+chr1	146999	.	T	G	0	.	AC=0

cyvcf2/tests/test_reader.py

@@ -268,6 +268,18 @@ def test_writer_from_string():
     w.write_record(v)
     w.close()
 
+def test_isa():
+
+    vcf = VCF(os.path.join(HERE, "test.isa.vcf"))
+    for i, v in enumerate(vcf):
+        if i in {0, 1, 2, 3}:
+            assert v.is_indel
+            assert not v.is_snp
+        if i in {4}:
+            assert v.is_snp
+
+
+
 
 def run_writer(writer, filename, rec):
     rec.INFO["AC"] = "3"