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Hoogenboom
fdstools
Commits
fd596525
Commit
fd596525
authored
Mar 15, 2017
by
Hoogenboom, Jerry
Browse files
Release FDSTools v1.1.1 (TSSV 1.1.1)
Fixing a bug (introduced in v1.1.0) in the TSSV report output file.
parent
b80e9427
Changes
3
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README.rst
View file @
fd596525
...
...
@@ -29,6 +29,9 @@ Alternatively, FDSTools can be installed by running:
FDSTools Changelog
------------------
v1.1.1
- Includes TSSV v1.1.1
v1.1.0
- Allele name heuristics: don't produce insertions at the end of the prefix
or at the beginning of the suffix; just include extra STR blocks.
...
...
@@ -473,6 +476,11 @@ v1.0.0
TSSV
~~~~
v1.1.1
- Fixed incorrect calculation of tLeft, fLeft, rLeft, tRight and fRight
columns in the report output file when -T/--num-threads was set to 2 or
higher. The primary output of was unaffected.
v1.1.0
- Added option '-T/--num-threads' (default: 1), which controls the number
of worker threads TSSV may spawn to run the analysis in parallel.
...
...
fdstools/__init__.py
View file @
fd596525
...
...
@@ -24,7 +24,7 @@ including tools for characterisation and filtering of PCR stutter artefacts and
other systemic noise, and for automatic detection of the alleles in a sample.
"""
__version_info__
=
(
'1'
,
'1'
,
'
0
'
)
__version_info__
=
(
'1'
,
'1'
,
'
1
'
)
__version__
=
'.'
.
join
(
__version_info__
)
usage
=
__doc__
.
split
(
"
\n\n\n
"
)
...
...
fdstools/tools/tssv.py
View file @
fd596525
...
...
@@ -47,7 +47,7 @@ from ..lib import pos_int_arg, add_input_output_args, get_input_output_files,\
add_sequence_format_args
,
reverse_complement
,
PAT_SEQ_RAW
,
\
get_column_ids
,
ensure_sequence_format
__version__
=
"1.1.
0
"
__version__
=
"1.1.
1
"
# Default values for parameters are specified below.
...
...
@@ -231,10 +231,10 @@ def process_file_parallel(infile, tssv_library, indel_score, workers):
for
marker
,
matches
,
seq1
,
seq2
in
results
:
recognised
|=
matches
counters
[
marker
][
"fLeft"
]
+=
matches
counters
[
marker
][
"fRight"
]
+=
(
matches
>>
1
)
counters
[
marker
][
"rLeft"
]
+=
(
matches
>>
2
)
counters
[
marker
][
"rRight"
]
+=
(
matches
>>
3
)
counters
[
marker
][
"fLeft"
]
+=
matches
&
1
counters
[
marker
][
"fRight"
]
+=
matches
>>
1
&
1
counters
[
marker
][
"rLeft"
]
+=
matches
>>
2
&
1
counters
[
marker
][
"rRight"
]
+=
matches
>>
3
&
1
# Search in the forward strand.
if
seq1
is
not
None
:
...
...
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