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Blaise LI
libhts
Commits
3d62098c
Commit
3d62098c
authored
Nov 15, 2018
by
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
Changes
1
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libhts/libhts.py
View file @
3d62098c
...
...
@@ -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"
:
...
...
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