Commit 68caf656 authored by Hoogenboom, Jerry's avatar Hoogenboom, Jerry

Update changelog in README.rst

parent 08cf6ddd
......@@ -29,6 +29,31 @@ Alternatively, FDSTools can be installed by running:
FDSTools Changelog
------------------
v0.0.4
- FDSTools will now print profiling information to stdout when the
-d/--debug option was specified.
- Fixed bug where specifying '-' as the output filename would be taken
literally, while it should have been interpreted as 'write to standard
out' (Affected tools: BGCorrect, Samplestats, Seqconvert, Stuttermark).
- Added more detailed license information to FDSTools.
- Updated bundled JavaScript library Vega to v2.6.0
- Updated bundled JavaScript library D3 to v3.5.17
- Includes BGCorrect v1.0.1
- Includes BGEstimate v1.1.0
- Includes BGMerge v1.0.1
- Includes BGPredict v1.0.1
- Includes Libconvert v1.0.1
- Includes Samplestats v1.0.1
- Includes Seqconvert v1.0.1
- Includes Stuttermodel v1.1.0
- Includes TSSV v1.0.1
- Includes Vis v1.0.1
- Includes Allelevis v1.0.0beta2
- Includes BGRawvis v1.0.1
- Includes Profilevis v1.0.1
- Includes Samplevis v2.0.1
- Includes Stuttermodelvis v1.0.0beta2
v0.0.3
- Updated bundled JavaScript library Vega to v2.5.0
- Updated bundled JavaScript library D3 to v3.5.12
......@@ -71,12 +96,29 @@ v1.0.0
BGCorrect
~~~~~~~~~
v1.0.1
- Added new column 'weight' to the output. The value in this column
expresses the number of times that the noise profile of that allele
fitted in the sample.
v1.0.0
- Initial version
BGEstimate
~~~~~~~~~~
v1.1.0
- Added a new option -g/--min-genotypes (default: 3). Only alleles that
occur in at least this number of unique heterozygous genotypes will be
considered. This is to avoid 'contamination' of the noise profile of one
allele with the noise of another. If homozygous samples are available for
an allele, this filter is not applied to that allele. Setting this option
to 1 effectively disables it. This option has the same cascading effect
as the -s/--min-samples option, that is, if one allele does not meet the
threshold, the samples with this allele are excluded which may cause some
of the other alleles of these samples to fall below the threshold as
well.
v1.0.0
- Initial version
......@@ -95,12 +137,23 @@ v1.0.0
BGMerge
~~~~~~~
v1.0.1
- Reduced memory usage
v1.0.0
- Initial version
BGPredict
~~~~~~~~~
v1.0.1
- Greatly reduced memory usage.
- BGPredict will now output nonzero values below the threshold set by
-n/--min-pct if the predicted noise ratio of the same stutter on the
other strand is above the threshold. Previously, values below the
threshold were clipped to zero, which may cause unnecessarily high strand
bias in the predicted profile.
v1.0.0
- Initial version
......@@ -119,18 +172,43 @@ v1.0.0
Libconvert
~~~~~~~~~~
v1.0.1
- Specifying '-' as the first positional argument to libconvert will now
correctly interpret this as "read from stdin" instead of throwing a "file
not found" error (or reading from a file named "-" if it exists)
v1.0.0
- Initial version
Samplestats
~~~~~~~~~~~
v1.0.1
- Samplestats will now round to 4 or 5 significant digits if a value is
above 1000 or 10000, respectively. Previously, this was only done for the
combined 'Other sequences' values
- The 'Other sequences' lines will now also include values for
total_recovery, forward_recovery, and reverse_recovery
- The total_recovery, forward_recovery, and reverse_recovery columns are no
longer placed to the left of all the other columns generated by
Samplestats
- The help text for Samplestats erroneously listed the X_recovery_pct
instead of X_recovery
- Added support for the new 'weight' column produced by BGCorrect when the
-a/--filter-action option is set to 'combine'
v1.0.0
- Initial version
Seqconvert
~~~~~~~~~~
v1.0.1
- Internal naming of the first positional argument was changed from
'format' to 'sequence-format'. This was done for consistency with the
-F/--sequence-format option in other tools, giving it the same name in
Pipeline configuration files.
v1.0.0
- Initial version
......@@ -170,48 +248,122 @@ v1.0.0
Stuttermodel
~~~~~~~~~~~~
v1.1.0
- Stuttermodel will now only output a fit for one strand if it could also
obtain a fit for the other strand (for the same marker, unit, and stutter
depth). This new behaviour can be disabled with a new -O/--orphans
option.
- Fixed bug that caused Stuttermodel to output only the raw data points for
-1 and +1 stutter when normal output was supressed
v1.0.0
- Initial version
TSSV
~~~~
v1.0.1
- Renamed the '--is_fastq' option to '--is-fastq', which was the only
option with an underscore instead of a hyphen in FDSTools
- Fixed crash that would occur if -F/--sequence-format was set to anything
other than 'raw'
v1.0.0
- Initial version
Vis
~~~
v1.0.1
- Added -j/--jitter option for Stuttermodelvis (default: 0.25)
- Fixed bug where Vis would not allow the -n/--min-abs and the
-s/--min-per-strand options to be set to 0
v1.0.0
- Initial version
Allelevis
~~~~~~~~~
v1.0.0beta2
- Fixed potential crash/corruption that could occur with very unfortunate
combinations of sample names and marker names
- HTML visualisations made with the -O/--online option of the Vis tool will
now contain https URLs instead of http
- Added two more colours to the legend, such that a maximum of 22 markers
is now supported without re-using colours
v1.0.0beta1
- Initial version
BGRawvis
~~~~~~~~
v1.0.1
- Fixed a JavaScript crash that would occur in HTML visualisations if the
Marker name filter resulted in an invalid regular expression (e.g., when
the entered value ends with a backslash)
- Reduced Vega graph spec complexity by using the new Rank transform to
position the subgraphs
- HTML visualisations made with the -O/--online option of the Vis tool will
now contain https URLs instead of http
v1.0.0
- Initial version
Profilevis
~~~~~~~~~~
v1.0.1
- Fixed a JavaScript crash that would occur in HTML visualisations if the
Marker name filter resulted in an invalid regular expression (e.g., when
the entered value ends with a backslash)
- Reduced Vega graph spec complexity by using the new Rank transform to
position the subgraphs.
- HTML visualisations made with the -O/--online option of the Vis tool will
now contain https URLs instead of http
v1.0.0
- Initial version
Samplevis
~~~~~~~~~
v2.0.1
- Fixed a JavaScript crash that would occur in HTML visualisations if the
Marker name filter resulted in an invalid regular expression (e.g., when
the entered value ends with a backslash)
- Reduced Vega graph spec complexity by using the new Rank transform to
position the subgraphs
- Fixed a glitch in HTML visualisations where clicking the 'Truncate
sequences to' label would select the marker spacing input
- In HTML visualisations, the 'Notes' table cells with 'BGPredict' in them
now get a light orange background to warn the user that their background
profile was computed. If a sequence was explicitly 'not corrected', 'not
in ref db', or 'corrected as background only', the same colour is used.
- The message bar at the bottom of Samplevis HTML visualisations will now
grow no larger than 3 lines. A scroll bar will appear as needed.
- HTML visualisations made with the -O/--online option of the Vis tool will
now contain https URLs instead of http
v2.0.0
- Initial version
Stuttermodelvis
~~~~~~~~~~~~~~~
v1.0.0beta2
- HTML visualisations now support drawing raw data points on top of the fit
functions. The points can be drawn with an adjustable jitter to reduce
overlap.
- Fixed a JavaScript crash that would occur in HTML visualisations if the
Repeat unit or Marker name filter resulted in an invalid regular
expression (e.g., when the entered value ends with a backslash)
- Reduced Vega graph spec complexity by using the new Rank transform to
position the subgraphs.
- HTML visualisations made with the -O/--online option of the Vis tool will
now contain https URLs instead of http
v1.0.0beta1
- Initial version
......
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