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Blaise LI
libhts
Commits
3d62098c
Commit
3d62098c
authored
6 years ago
by
Blaise Li
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Switched to new small RNA classification.
This is not yet fully tested, and may have effects on other pipelines.
parent
2807a83a
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libhts/libhts.py
+5
-2
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libhts/libhts.py
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libhts/libhts.py
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3d62098c
...
@@ -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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