Set type of variants in uppercase

build_results.py

@@ -890,7 +890,7 @@ def add_jupyter_header(records: dict, groups: list, type_v: str, jupyter_file: s
         jupy_f.write(json.dumps(jupy, indent=4))
 
 
-def init(output, vcf_files, true_vcf, rules, filtered_vcfs=None, type_v="del", overlap_cutoff=0.5,
+def init(output, vcf_files, true_vcf, rules, filtered_vcfs=None, type_v="DEL", overlap_cutoff=0.5,
          left_precision=sys.maxsize, right_precision=sys.maxsize, no_xls=False, haploid=False):
 
     if not os.path.exists(output):

lib/vcf.py

@@ -7,7 +7,7 @@ sys.path.insert(0, os.path.join(prg_path, "svlib"))
 from svreader.vcfwrapper import VCFReader
 
 
-ALLOW_VARIANTS = ['del', 'inv']
+ALLOW_VARIANTS = ['DEL', 'INV']
 
 
 def passed_variant(record):
@@ -19,7 +19,7 @@ def passed_variant(record):
     return record.filter is None or len(record.filter) == 0 or "PASS" in record.filter
 
 
-def readvariants(vcffile: str, type_v, variants: dict=None, dofilter: bool=False, all_variants: dict=None):
+def readvariants(vcffile: str, type_v:str, variants: dict=None, dofilter: bool=False, all_variants: dict=None):
     """
     Read variants from a VCF file
     :param vcffile: input vcf file
@@ -31,12 +31,12 @@ def readvariants(vcffile: str, type_v, variants: dict=None, dofilter: bool=False
     """
     if variants is None:
         variants = {}
-    if type_v.lower() not in ALLOW_VARIANTS:
+    if type_v.upper() not in ALLOW_VARIANTS:
         raise ValueError("Invalid variant type: %s" % type_v)
 
     vcfin = VCFReader(vcffile)
     for r in vcfin:
-        if r.sv_type.lower() == type_v:
+        if r.sv_type.upper() == type_v:
             if not dofilter or passed_variant(r):
                 variants[r.id] = r
             if dofilter and all_variants is not None: