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Hoogenboom
fdstools
Commits
53fbe9ec
Commit
53fbe9ec
authored
Mar 09, 2016
by
Hoogenboom, Jerry
Browse files
Fix allelefinder allowing 'Other sequences' as allele
parent
da8d1d1b
Changes
2
Hide whitespace changes
Inline
Side-by-side
fdstools/tools/allelefinder.py
View file @
53fbe9ec
...
...
@@ -81,7 +81,7 @@ def find_alleles_sample(data, outfile, reportfile, tag, min_reads,
top_allele
[
marker
]
=
0
top_noise
[
marker
]
=
[
"-"
,
0
]
if
sequence
==
"Other
S
equences"
and
reads
>=
top_noise
[
marker
][
1
]:
if
sequence
==
"Other
s
equences"
and
reads
>=
top_noise
[
marker
][
1
]:
# Aggregated sequences are new highest noise!
top_noise
[
marker
]
=
[
sequence
,
reads
]
elif
reads
>
top_allele
[
marker
]:
...
...
notes.txt
View file @
53fbe9ec
...
...
@@ -190,6 +190,15 @@ name tssv OK
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Tool and visualisation version numbering, e.g., v1.2.3:
1 major version, changes only with large, disruptive, fundamental changes
2 minor version, changes when the default output is altered, or when it is
otherwise likely that user pipelines will break when updating
3 patch version, changes with any other changes (bug fixes, new optional
features, etc.)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Find TODOs and FIXMEs in the code:
grep "TODO\|FIXME" *.py */*.py */*/*.py
...
...
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