diff --git a/trtools/utils/tr_harmonizer.py b/trtools/utils/tr_harmonizer.py index a2bdd5ae..e9629b50 100644 --- a/trtools/utils/tr_harmonizer.py +++ b/trtools/utils/tr_harmonizer.py @@ -327,7 +327,7 @@ def _HarmonizeHipSTRRecord(vcfrecord: cyvcf2.Variant): or vcfrecord.INFO.get('END') is None or vcfrecord.INFO.get('PERIOD') is None): raise TypeError( - "Record at {}:{} is missing one of the mandatory HipSTR info fields START, END, PERIOD".format(vcfrecord.CHROM, vcfrecord.POS) + _beagle_error + "Record at {}:{} is missing one of the mandatory HipSTR info fields START, END, PERIOD. ".format(vcfrecord.CHROM, vcfrecord.POS) + _beagle_error ) # determine full alleles and trimmed alleles pos = int(vcfrecord.POS) @@ -403,7 +403,7 @@ def _HarmonizeAdVNTRRecord(vcfrecord: cyvcf2.Variant): """ if vcfrecord.INFO.get('RU') is None or vcfrecord.INFO.get('VID') is None: raise TypeError( - "Record at {}:{} is missing one of the mandatory ADVNTR info fields RU, VID".format(vcfrecord.CHROM, vcfrecord.POS) + _beagle_error + "Record at {}:{} is missing one of the mandatory ADVNTR info fields RU, VID. ".format(vcfrecord.CHROM, vcfrecord.POS) + _beagle_error ) ref_allele = vcfrecord.REF.upper() if vcfrecord.ALT: @@ -507,7 +507,7 @@ def _HarmonizeEHRecord(vcfrecord: cyvcf2.Variant): """ if vcfrecord.INFO.get('VARID') is None or vcfrecord.INFO.get('RU') is None: raise TypeError( - "Record at {}:{} is missing one of the mandatory ExpansionHunter info fields VARID, RU".format(vcfrecord.CHROM, vcfrecord.POS) + "Record at {}:{} is missing one of the mandatory ExpansionHunter info fields VARID, RU. ".format(vcfrecord.CHROM, vcfrecord.POS) + _beagle_error ) record_id = vcfrecord.INFO["VARID"]