From b2a03fc6b660e2efce6cf3dc47ecaccdae317161 Mon Sep 17 00:00:00 2001 From: chapmanb Date: Wed, 31 Jan 2018 15:07:20 -0500 Subject: [PATCH] GEMINI: separate symlinked effects decomposition Follow up to https://github.com/chapmanb/bcbio-nextgen/commit/c575ab3f8012f83cfc490be0c766cb4ec634e7f6 which also names the symlinks correct for effects and no effects. Fixes #2225 --- bcbio/variation/normalize.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/bcbio/variation/normalize.py b/bcbio/variation/normalize.py index 242a0429e..469820fb6 100644 --- a/bcbio/variation/normalize.py +++ b/bcbio/variation/normalize.py @@ -58,7 +58,10 @@ def normalize(in_file, data, passonly=False, normalize_indels=True, split_bialle rerun_effects=True, remove_oldeffects=False): """Normalizes variants and reruns SnpEFF for resulting VCF """ - out_file = "%s-nomultiallelic%s" % utils.splitext_plus(in_file) + if remove_oldeffects: + out_file = "%s-noeff-nomultiallelic%s" % utils.splitext_plus(in_file) + else: + out_file = "%s-nomultiallelic%s" % utils.splitext_plus(in_file) if not utils.file_exists(out_file): if vcfutils.vcf_has_variants(in_file): ready_ma_file = _normalize(in_file, data, passonly=passonly,