From 2981bd23feaf0ffc026d2b3be1662f6c3edc4119 Mon Sep 17 00:00:00 2001 From: Sebastian Proost Date: Mon, 29 Aug 2016 09:59:58 +0200 Subject: [PATCH] checks to prevent qc to fail on empty samples --- pipeline/check/quality.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pipeline/check/quality.py b/pipeline/check/quality.py index 64fe6e7..d5422a6 100644 --- a/pipeline/check/quality.py +++ b/pipeline/check/quality.py @@ -55,7 +55,8 @@ def check_htseq(filename, cutoff=0, log=None): total = sum([mapped_reads, values['__no_feature'] if '__no_feature' in values.keys() else 0, - values['__ambiguous'] if '__ambiguous' in values.keys() else 0]) + values['__ambiguous'] if '__ambiguous' in values.keys() else 0] + ) percentage_mapped = ((mapped_reads*100)/total) if total > 0 else 0