Commit b80e9427 authored by Hoogenboom, Jerry's avatar Hoogenboom, Jerry
Browse files

Release v1.1.0

parent be8dbe46
...@@ -29,6 +29,38 @@ Alternatively, FDSTools can be installed by running: ...@@ -29,6 +29,38 @@ Alternatively, FDSTools can be installed by running:
FDSTools Changelog FDSTools Changelog
------------------ ------------------
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.
- FDSTools will no longer crash with a 'column not found' error when
an input file is empty. This situation is now treated as if the
expected columns existed, but no lines of actual data were present.
This greatly helps in tracking down issues in pipelines involving
multiple tools, as tools will now shutdown gracefully if an upstream
tool fails to write output.
- Includes Allelefinder v1.0.1
- Includes BGAnalyse v1.0.1
- Includes BGCorrect v1.0.2
- Includes BGEstimate v1.1.2
- Includes BGHomRaw v1.0.1
- Includes BGHomStats v1.0.1
- Includes BGMerge v1.0.3
- Includes BGPredict v1.0.2
- Includes FindNewAlleles v1.0.1
- Includes Libconvert v1.1.2
- Includes Library v1.0.3
- Includes Pipeline v1.0.3
- Includes Samplestats v1.1.1
- Includes Seqconvert v1.0.2
- Includes Stuttermark v1.5.1
- Includes Stuttermodel v1.1.2
- Includes TSSV v1.1.0
- Includes Vis v1.0.4
- Includes BGRawvis v2.0.1
- Includes Profilevis v2.0.1
- Includes Samplevis v2.2.0
- Includes Stuttermodelvis v2.0.3
v1.0.1 v1.0.1
- Fixed crash that occurred when using the -i option to run the same - Fixed crash that occurred when using the -i option to run the same
command on multiple input files. command on multiple input files.
...@@ -145,18 +177,30 @@ v0.0.1 ...@@ -145,18 +177,30 @@ v0.0.1
Allelefinder Allelefinder
~~~~~~~~~~~~ ~~~~~~~~~~~~
v1.0.1
- Fixed crash that occurred when converting sequences to allele name format
when no library file was provided.
- Shut down cleanly when the output pipe is closed.
v1.0.0 v1.0.0
- Initial version - Initial version
BGAnalyse BGAnalyse
~~~~~~~~~ ~~~~~~~~~
v1.0.1
- Shut down cleanly when the output pipe is closed.
v1.0.0 v1.0.0
- Initial version - Initial version
BGCorrect BGCorrect
~~~~~~~~~ ~~~~~~~~~
v1.0.2
- Don't crash on empty input files.
- Shut down cleanly when the output pipe is closed.
v1.0.1 v1.0.1
- Added new column 'weight' to the output. The value in this column - Added new column 'weight' to the output. The value in this column
expresses the number of times that the noise profile of that allele expresses the number of times that the noise profile of that allele
...@@ -168,6 +212,9 @@ v1.0.0 ...@@ -168,6 +212,9 @@ v1.0.0
BGEstimate BGEstimate
~~~~~~~~~~ ~~~~~~~~~~
v1.1.2
- Shut down cleanly when the output pipe is closed.
v1.1.1 v1.1.1
- Added option -p/--profiles which can be used to provide a previously - Added option -p/--profiles which can be used to provide a previously
created background noise profiles file, from which starting values will created background noise profiles file, from which starting values will
...@@ -191,18 +238,31 @@ v1.0.0 ...@@ -191,18 +238,31 @@ v1.0.0
BGHomRaw BGHomRaw
~~~~~~~~ ~~~~~~~~
v1.0.1
- Clarified the 'Allele x of marker y has 0 reads' error message with the
name of the sample that triggered the error.
- Shut down cleanly when the output pipe is closed.
v1.0.0 v1.0.0
- Initial version - Initial version
BGHomStats BGHomStats
~~~~~~~~~~ ~~~~~~~~~~
v1.0.1
- Error messages about the input data now contain the name of the sample
that triggered the error.
- Shut down cleanly when the output pipe is closed.
v1.0.0 v1.0.0
- Initial version - Initial version
BGMerge BGMerge
~~~~~~~ ~~~~~~~
v1.0.3
- Shut down cleanly when the output pipe is closed.
v1.0.2 v1.0.2
- Minor changes to facilitate explicit filename wildcard support - Minor changes to facilitate explicit filename wildcard support
...@@ -215,6 +275,10 @@ v1.0.0 ...@@ -215,6 +275,10 @@ v1.0.0
BGPredict BGPredict
~~~~~~~~~ ~~~~~~~~~
v1.0.2
- Don't crash on empty input files.
- Shut down cleanly when the output pipe is closed.
v1.0.1 v1.0.1
- Greatly reduced memory usage. - Greatly reduced memory usage.
- BGPredict will now output nonzero values below the threshold set by - BGPredict will now output nonzero values below the threshold set by
...@@ -229,13 +293,20 @@ v1.0.0 ...@@ -229,13 +293,20 @@ v1.0.0
FindNewAlleles FindNewAlleles
~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
v1.0.1
- Don't crash on empty input files.
- Shut down cleanly when the output pipe is closed.
v1.0.0 v1.0.0
- Initial version - Initial version
Libconvert Libconvert
~~~~~~~~~~ ~~~~~~~~~~
v1.1.1: v1.1.2
- Shut down cleanly when the output pipe is closed.
v1.1.1
- Adjustments for supporting IUPAC notation in prefix and suffix sequences - Adjustments for supporting IUPAC notation in prefix and suffix sequences
when converting from FDSTools to TSSV library format. when converting from FDSTools to TSSV library format.
...@@ -262,6 +333,9 @@ v1.0.0 ...@@ -262,6 +333,9 @@ v1.0.0
Library Library
~~~~~~~ ~~~~~~~
v1.0.3
- Shut down cleanly when the output pipe is closed.
v1.0.2 v1.0.2
- Added documentation for IUPAC support to the descriptive comment of the - Added documentation for IUPAC support to the descriptive comment of the
[prefix] section. [prefix] section.
...@@ -276,6 +350,10 @@ v1.0.0 ...@@ -276,6 +350,10 @@ v1.0.0
Pipeline Pipeline
~~~~~~~~ ~~~~~~~~
v1.0.3
- Fixed glitch that caused the 'bgprofiles.html' output file of the
reference-database analysis to lack a proper title.
v1.0.2 v1.0.2
- Added -A/--in-allelelist option, with which an existing allele list file - Added -A/--in-allelelist option, with which an existing allele list file
can be provided when running the reference-database analysis pipeline, can be provided when running the reference-database analysis pipeline,
...@@ -293,6 +371,10 @@ v1.0.0 ...@@ -293,6 +371,10 @@ v1.0.0
Samplestats Samplestats
~~~~~~~~~~~ ~~~~~~~~~~~
v1.1.1
- Don't crash on empty input files.
- Shut down cleanly when the output pipe is closed.
v1.1.0 v1.1.0
- Changed default allele calling option thresholds: - Changed default allele calling option thresholds:
- Changed default value of -m/--min-pct-of-max from 5.0 to 2.0 - Changed default value of -m/--min-pct-of-max from 5.0 to 2.0
...@@ -319,6 +401,9 @@ v1.0.0 ...@@ -319,6 +401,9 @@ v1.0.0
Seqconvert Seqconvert
~~~~~~~~~~ ~~~~~~~~~~
v1.0.2
- Shut down cleanly when the output pipe is closed.
v1.0.1 v1.0.1
- Internal naming of the first positional argument was changed from - Internal naming of the first positional argument was changed from
'format' to 'sequence-format'. This was done for consistency with the 'format' to 'sequence-format'. This was done for consistency with the
...@@ -331,6 +416,10 @@ v1.0.0 ...@@ -331,6 +416,10 @@ v1.0.0
Stuttermark Stuttermark
~~~~~~~~~~~ ~~~~~~~~~~~
v1.5.1
- Don't crash on empty input files.
- Shut down cleanly when the output pipe is closed.
v1.5.0 v1.5.0
- Changed column names 'name' and 'allele' to 'marker' and 'sequence', - Changed column names 'name' and 'allele' to 'marker' and 'sequence',
respectively. WARNING: Stuttermark is now INCOMPATIBLE with output respectively. WARNING: Stuttermark is now INCOMPATIBLE with output
...@@ -364,6 +453,9 @@ v1.0.0 ...@@ -364,6 +453,9 @@ v1.0.0
Stuttermodel Stuttermodel
~~~~~~~~~~~~ ~~~~~~~~~~~~
v1.1.2
- Shut down cleanly when the output pipe is closed.
v1.1.1 v1.1.1
- Minor change to internal variant representation - Minor change to internal variant representation
...@@ -381,6 +473,11 @@ v1.0.0 ...@@ -381,6 +473,11 @@ v1.0.0
TSSV TSSV
~~~~ ~~~~
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.
- Shut down cleanly when the output pipe is closed.
v1.0.2 v1.0.2
- Added new option -n/--indel-score which can be used to increase the - Added new option -n/--indel-score which can be used to increase the
penalty given to insertions and deletions in the flanking sequences penalty given to insertions and deletions in the flanking sequences
...@@ -399,6 +496,9 @@ v1.0.0 ...@@ -399,6 +496,9 @@ v1.0.0
Vis Vis
~~~ ~~~
v1.0.4
- Shut down cleanly when the output pipe is closed.
v1.0.3 v1.0.3
- The -n/--min-abs and -s/--min-per-strand options now accept non-integer - The -n/--min-abs and -s/--min-per-strand options now accept non-integer
values as well. values as well.
...@@ -452,6 +552,12 @@ v1.0.0 ...@@ -452,6 +552,12 @@ v1.0.0
BGRawvis BGRawvis
~~~~~~~~ ~~~~~~~~
v2.0.1
- Changed default save filename in HTML visualisations to 'bgprofiles-raw'.
- Fixed glitch where, in HTML visualisations with embedded data and a
custom title, the custom title was truncated to the last '.' as if it
were a file name.
v2.0.0 v2.0.0
- Replaced the simple Options overlay with responsive design options panels - Replaced the simple Options overlay with responsive design options panels
in HTML visualisations in HTML visualisations
...@@ -474,6 +580,12 @@ v1.0.0 ...@@ -474,6 +580,12 @@ v1.0.0
Profilevis Profilevis
~~~~~~~~~~ ~~~~~~~~~~
v2.0.1
- Changed default save filename in HTML visualisations to 'bgprofiles'.
- Fixed glitch where, in HTML visualisations with embedded data and a
custom title, the custom title was truncated to the last '.' as if it
were a file name.
v2.0.0 v2.0.0
- Replaced the simple Options overlay with responsive design options panels - Replaced the simple Options overlay with responsive design options panels
in HTML visualisations in HTML visualisations
...@@ -496,6 +608,13 @@ v1.0.0 ...@@ -496,6 +608,13 @@ v1.0.0
Samplevis Samplevis
~~~~~~~~~ ~~~~~~~~~
v2.2.0
- Fixed incorrect calculation of 'percentage of highest' if the 'sequence'
with the highest read count within a marker is the aggregated 'Other
sequences' data. In exceptional cases, this could have resulted in the
erroneous omission of an allele in the visualisation (graphs and/or
tables).
v2.1.2 v2.1.2
- Added 'Save page' link to HTML visualisations, which offers for download - Added 'Save page' link to HTML visualisations, which offers for download
a copy of the entire HTML visualisation including the user's changes. a copy of the entire HTML visualisation including the user's changes.
...@@ -547,6 +666,13 @@ v2.0.0 ...@@ -547,6 +666,13 @@ v2.0.0
Stuttermodelvis Stuttermodelvis
~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~
v2.0.3
- Fixed bug that caused HTML visualisations with embedded data to fail
while loading.
- Fixed glitch where, in HTML visualisations with embedded data and a
custom title, the custom title was truncated to the last '.' as if it
were a file name.
v2.0.2 v2.0.2
- Added filtering option for the stutter amount (-1, +1, -2, etc.). - Added filtering option for the stutter amount (-1, +1, -2, etc.).
- Added filtering option for the coefficient of determination (r squared - Added filtering option for the coefficient of determination (r squared
......
...@@ -24,7 +24,7 @@ including tools for characterisation and filtering of PCR stutter artefacts and ...@@ -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. other systemic noise, and for automatic detection of the alleles in a sample.
""" """
__version_info__ = ('1', '1', '0', 'dev3') __version_info__ = ('1', '1', '0')
__version__ = '.'.join(__version_info__) __version__ = '.'.join(__version_info__)
usage = __doc__.split("\n\n\n") usage = __doc__.split("\n\n\n")
......
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