Commit 3d62098c authored by Blaise Li's avatar Blaise Li
Browse files

Switched to new small RNA classification.

This is not yet fully tested, and may have effects on other pipelines.
parent 2807a83a
...@@ -275,8 +275,11 @@ def aligner2min_mapq(aligner, wildcards): ...@@ -275,8 +275,11 @@ def aligner2min_mapq(aligner, wildcards):
What minimal MAPQ value should a read have to be considered uniquely mapped? 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/>. See <https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/>.
""" """
mapped_type = wildcards.mapped_type try:
if mapped_type.startswith("unique_"): mapping_type = wildcards.mapping_type
except AttributeError:
mapping_type = wildcards.mapped_type
if mapping_type.startswith("unique_"):
if aligner == "hisat2": if aligner == "hisat2":
return "-Q 60" return "-Q 60"
elif aligner == "bowtie2": elif aligner == "bowtie2":
......
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