From 3d62098c759c1108aca1b36dddb369093fd5a8d5 Mon Sep 17 00:00:00 2001 From: Blaise Li <blaise.li__git@nsup.org> Date: Thu, 15 Nov 2018 20:12:08 +0100 Subject: [PATCH] Switched to new small RNA classification. This is not yet fully tested, and may have effects on other pipelines. --- libhts/libhts.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/libhts/libhts.py b/libhts/libhts.py index fa2deb7..5b4e1b0 100644 --- a/libhts/libhts.py +++ b/libhts/libhts.py @@ -275,8 +275,11 @@ def aligner2min_mapq(aligner, wildcards): What minimal MAPQ value should a read have to be considered uniquely mapped? See <https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/>. """ - mapped_type = wildcards.mapped_type - if mapped_type.startswith("unique_"): + try: + mapping_type = wildcards.mapping_type + except AttributeError: + mapping_type = wildcards.mapped_type + if mapping_type.startswith("unique_"): if aligner == "hisat2": return "-Q 60" elif aligner == "bowtie2": -- GitLab