Commit bbb08573 authored by Hoogenboom, Jerry's avatar Hoogenboom, Jerry

Release v1.0.1

parent 14b17206
......@@ -29,7 +29,30 @@ Alternatively, FDSTools can be installed by running:
FDSTools Changelog
------------------
v1.0.0rc1
v1.0.1
- Fixed crash that occurred when using the -i option to run the same
command on multiple input files.
- The 'usage' line now always starts with 'fdstools', even if FDSTools was
invoked through some other command (e.g. on Windows, FDSTools gets
invoked through a file called 'fdstools-script.py').
- Fixed bug with the -d/--debug option being ignored if placed before the
tool name on systems running Python 2.7.9 or later.
- FDSTools library files may now contain IUPAC ambiguous bases in the
prefix and suffix sequences of STR markers (except the first sequence,
as it is used as the reference). Additionally, optional bases may be
represented by lowercase letters.
- If no explicit prefix/suffix is given for an alias, the prefix/suffix of
the corresponding marker is assumed instead. This situation was not
handled correctly when converting from raw sequences to TSSV or
allelename format, which resulted in the alias remaining unused.
- Includes Libconvert v1.1.1
- Includes Library v1.0.2
- Includes Pipeline v1.0.2
- Includes Vis v1.0.3
- Includes Samplevis v2.1.2
- Includes Stuttermodelvis v2.0.2
v1.0.0
- Fixed bug that caused variant descriptions in allele names of non-STR
markers to be prepended with plus signs similar to suffix variants
in STR markers; when attempting to convert these allele names back to raw
......@@ -212,6 +235,10 @@ v1.0.0
Libconvert
~~~~~~~~~~
v1.1.1:
- Adjustments for supporting IUPAC notation in prefix and suffix sequences
when converting from FDSTools to TSSV library format.
v1.1.0
- When converting to FDSTools format, Libconvert automatically creates an
empty FDSTools library file with the same contents as what would be
......@@ -235,6 +262,10 @@ v1.0.0
Library
~~~~~~~
v1.0.2
- Added documentation for IUPAC support to the descriptive comment of the
[prefix] section.
v1.0.1
- Updated some of the comments describing the sections
- Added proper examples for non-STR markers and aliases
......@@ -245,6 +276,11 @@ v1.0.0
Pipeline
~~~~~~~~
v1.0.2
- Added -A/--in-allelelist option, with which an existing allele list file
can be provided when running the reference-database analysis pipeline,
bypassing Allelefinder.
v1.0.1
- Removed checking of the existence of the files specified for the
-S/--in-samples option; instead, this is left to the downstream tools to
......@@ -363,6 +399,12 @@ v1.0.0
Vis
~~~
v1.0.3
- The -n/--min-abs and -s/--min-per-strand options now accept non-integer
values as well.
- Added six options to control the Table Filtering Options of Samplevis.
- Grouped some options as 'Display Options' in the command line help.
v1.0.2
- Changed default value of -n/--min-abs from 15 to 5
- Added -I/--input2 option, which allows for specifying a file with raw
......@@ -454,6 +496,13 @@ v1.0.0
Samplevis
~~~~~~~~~
v2.1.2
- Added 'Save page' link to HTML visualisations, which offers for download
a copy of the entire HTML visualisation including the user's changes.
- Added automatic allele calling to static visualisations.
- The net effect of the allele calling thresholds (table filtering options)
is now visualised in the graphs as a dashed vertical red line.
v2.1.1
- Added tooltip support to HTML visualisations
- The tooltip may include a 'new allele' note if the input sample was
......@@ -498,6 +547,11 @@ v2.0.0
Stuttermodelvis
~~~~~~~~~~~~~~~
v2.0.2
- Added filtering option for the stutter amount (-1, +1, -2, etc.).
- Added filtering option for the coefficient of determination (r squared
value) of the fit functions.
v2.0.1
- Changed the unit in the horizontal axis title from 'bp' to 'nt'
......
......@@ -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', '0', '1', 'dev3')
__version_info__ = ('1', '0', '1')
__version__ = '.'.join(__version_info__)
usage = __doc__.split("\n\n\n")
......
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