From c3a49442be91a0dfcee36ffb78daadc7d86facd2 Mon Sep 17 00:00:00 2001 From: Patrick Date: Fri, 10 Jan 2020 13:19:34 +0000 Subject: [PATCH 1/2] replaced int version parsing with hard check --- gelweb/gel2mdt/database_utils/case_handler.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gelweb/gel2mdt/database_utils/case_handler.py b/gelweb/gel2mdt/database_utils/case_handler.py index b86277a6..041d8073 100755 --- a/gelweb/gel2mdt/database_utils/case_handler.py +++ b/gelweb/gel2mdt/database_utils/case_handler.py @@ -292,7 +292,7 @@ def parse_ig_variants(self, ig_obj, genome_build, variant_object_count, case_var return ig_obj, case_variant_list, variant_object_count def parse_ig_svs(self, ig_obj, genome_build, case_sv_list): - if int(ig_obj.softwareVersions['gel-tiering'].replace('.', '')) <= 1000: + if ig_obj.softwareVersions['gel-tiering'] != '1.0.0': for variant in ig_obj.structuralVariants: variant.case_variant = False return ig_obj, case_sv_list @@ -318,7 +318,7 @@ def parse_ig_svs(self, ig_obj, genome_build, case_sv_list): return ig_obj, case_sv_list def parse_ig_strs(self, ig_obj, genome_build, case_str_list): - if int(ig_obj.softwareVersions['gel-tiering'].replace('.', '')) <= 1000: + if ig_obj.softwareVersions['gel-tiering'] != '1.0.0': for variant in ig_obj.shortTandemRepeats: variant.case_variant = False return ig_obj, case_str_list From 54428d8862624cc3e734a63794b49672298ec0cb Mon Sep 17 00:00:00 2001 From: Patrick Date: Sat, 11 Jan 2020 12:45:20 +0000 Subject: [PATCH 2/2] mistake in logic --- gelweb/gel2mdt/database_utils/case_handler.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gelweb/gel2mdt/database_utils/case_handler.py b/gelweb/gel2mdt/database_utils/case_handler.py index 041d8073..193f18f4 100755 --- a/gelweb/gel2mdt/database_utils/case_handler.py +++ b/gelweb/gel2mdt/database_utils/case_handler.py @@ -292,7 +292,7 @@ def parse_ig_variants(self, ig_obj, genome_build, variant_object_count, case_var return ig_obj, case_variant_list, variant_object_count def parse_ig_svs(self, ig_obj, genome_build, case_sv_list): - if ig_obj.softwareVersions['gel-tiering'] != '1.0.0': + if ig_obj.softwareVersions['gel-tiering'] == '1.0.0': for variant in ig_obj.structuralVariants: variant.case_variant = False return ig_obj, case_sv_list @@ -318,7 +318,7 @@ def parse_ig_svs(self, ig_obj, genome_build, case_sv_list): return ig_obj, case_sv_list def parse_ig_strs(self, ig_obj, genome_build, case_str_list): - if ig_obj.softwareVersions['gel-tiering'] != '1.0.0': + if ig_obj.softwareVersions['gel-tiering'] == '1.0.0': for variant in ig_obj.shortTandemRepeats: variant.case_variant = False return ig_obj, case_str_list