- 03 Oct, 2016 1 commit
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Hoogenboom, Jerry authored
* General changes in v1.0.0rc1: * 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 sequences, FDSTools would crash with an 'Invalid allele name' error. * Allelevis v2.0.1 (additionally): * In the tooltip in HTML visualisations, a line break may now only be inserted in allele names after an underscore character (_) or after a repeat block in STR allele names. If the input file contains raw sequences, line breaks may now be introduced anywhere in the sequence. * Samplevis v2.1.1: * Added tooltip support to HTML visualisations. Moving the mouse pointer over one of the alleles in the graph now displays a tooltip giving per-strand read counts of that allele. The tooltip may include a 'new allele' note if the input sample was analysed with FindNewAlleles. * The allele tables in HTML visualisations will now grow much wider than before if the screen (or window) is very narrow. * In the tables in HTML visualisations, a line break may now only be inserted in allele names after an underscore character (_) or after a repeat block in STR allele names. If the input file contains raw sequences, line breaks may now be introduced anywhere in the sequence. * Improved determination of column widths of the allele tables when printing an HTML visualisation. * When printing an HTML visualisation, the graph and the corresponding table of a marker will be kept on the same page in all browsers now. * Fixed glitch that caused 'Infinity%' or 'NaN%' to be written in some cells in the allele tables in HTML visualisations for sequences that had zero reads (before or after correction). These cells will remain empty now. * Pipeline v1.0.1 (additionally): * The Pipeline tool will now only write the command lines of the tools it runs if the -d/--debug option was specified. * Library v1.0.1 (additionally): * Added proper examples for non-STR markers and aliases. * Stuttermodel v1.1.1: * Minor change to internal variant representation.
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- 20 Sep, 2016 2 commits
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Hoogenboom, Jerry authored
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Hoogenboom, Jerry authored
* General changes in v0.0.6.dev1: * Tools that take a list of files as their argument (through the -i option or as positionals) now explicitly support glob patterns. This means they will interpret '*' and '?' characters as wildcards for 'zero or more characters' and 'any one character', respectively. On Unix-like systems this is generally done by the shell, but on Windows one had to specify every file name completely. * BGEstimate v1.1.1: * Added option -p/--profiles which can be used to provide a previously created background noise profiles file. BGEstimate will read starting values from this file instead of assuming zero noise. * BGMerge v1.0.2: * Small code changes to facilitate explicit glob pattern matching support. * Pipeline v1.0.1: * The Pipeline tool will no longer check the existence of the files specified for the -S/--in-samples option; instead, this is left to the downstream tools to find out, consistent with how this works with the other input file options. * Allelevis v2.0.1: * Added tooltip support to HTML visualisations. Moving the mouse pointer over a node or edge in the graph now displays a tooltip giving allele names and sample counts. * Stuttermodelvis v2.0.1: * Changed the unit in the horizontal axis title from 'bp' to 'nt'. * Library v1.0.1: * Updated some of the comments describing the sections.
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- 06 Sep, 2016 1 commit
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Hoogenboom, Jerry authored
* General changes in v0.0.5: * The TSSV tool now depends on version 0.4.0 of TSSV. * Added new Pipeline tool that runs one of three default analysis pipelines automatically given a configuration file with tool options and input/output file names. The three available pipeline options are 'reference-sample', analysing a single reference sample with TSSV and Stuttermark; 'reference-database', analysing a collection of reference samples with BGEstimate and Stuttermodel; and 'case-sample', analysing a single case sample with TSSV, BGPredict, BGMerge, BGCorrect, and Samplestats. * Added new Library tool that creates an empty FDSTools library file. Users may optionally specify the intented use of the library (STR markers, non-STR-markers, or both). Only the sections that apply to the given types of markers will be included in the output. The [aliases] section is not included by default, but an option is available to add it. * Added new tool BGAnalyse which can be used to analyse the remaining amount of noise in reference samples after correction. This tool is a more sensitive successor of the 'Blame' tool. * Added new visualisation BGAnalysevis for visualising data obtained from BGAnalyse. This visualisation allows for identifying unclean or otherwise suboptimal samples by comparing the lowest, highest, and/or total remaining noise after correction for each marker in each sample. * The Blame tool was removed in favour of BGAnalyse. * Libconvert v1.1.0: * When converting to FDSTools format, Libconvert automatically creates an empty FDSTools library file with the same contents as what would be obtained from the new Library tool without arguments. * The -a/--aliases option was modified such that it has the same effect as the -a/--aliases option of the new Library tool. This means that without this option specified, the [aliases] section will not be present in the output anymore. * The ability of the Libconvert tool to produce an empty FDSTools library file if no input file was given has been removed from the documentation (but not from the tool itself). * TSSV v1.0.2: * Added new option -n/--indel-score which can be used to increase the penalty given to insertions and deletions in the flanking sequences w.r.t. the penalty given to mismatches. * NOTE: Requires TSSV v0.4.0 or newer to be installed. * Vis 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 data points for Stuttermodelvis and Profilevis. * Added support for creating BGAnalysevis visualisations. * Profilevis v2.0.0: * Replaced the simple Options overlay with responsive design options panels in HTML visualisations. * Alleles and sequences are now sorted by CE allele length when applicable. * Added option to plot BGHomRaw data on top of the profiles. * Added marker selection menu for easier filtering. * BGRawvis v2.0.0: * Replaced the simple Options overlay with responsive design options panels in HTML visualisations. * Sequences are now sorted by CE allele length when applicable. * Changed default minimum number of reads from 15 to 5. * Added marker selection menu for easier filtering. * Stuttermodelvis v2.0.0: * Replaced the simple Options overlay with responsive design options panels in HTML visualisations. * Fixed glitch that caused the graphs to be re-rendered twice when loading a file by drag-and-drop in HTML visualisations. * Fixed glitch that made it possible to replace the data that was embedded in an HTML visualisation through drag-and-drop. * Added repeat unit selection menu for easier filtering. * Allelevis v2.0.0: * Replaced the simple Options overlay with responsive design options panels in HTML visualisations. * Reduced Vega graph spec complexity by using the new Rank transform to position the subgraphs. * Fixed glitch that caused unnecessary padding around the graph. * Samplestats v1.1.0: * 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 -p/--min-pct-of-sum from 3.0 to 1.5. * Mentioned allele calling in the tool descriptions. * Samplevis v2.1.0: * Changed default minimum number of reads for graph filtering from 15 to 5. * Changed default table filtering options: * Percentage of highest allele per marker changed from 5% to 2%. * Percentage of the marker's total reads changed from 3% to 1.5%. * Minimum number of reads in both orientations changed from 0 to 1.
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- 27 Jul, 2016 1 commit
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Hoogenboom, Jerry authored
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- 26 Jul, 2016 1 commit
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Hoogenboom, Jerry authored
* Global changes in 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. * 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. * 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. * 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. * 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'. * 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. * BGMerge v1.0.1: * Reduced memory usage. * TSSV v1.0.1: * Renamed the '--is_fastq' option to '--is-fastq'. It 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'. * 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). * 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. * Vis v1.0.1: * Added -j/--jitter option for Stuttermodelvis (default: 0.25). * Vis would not allow the -n/--min-abs and the -s/--min-per-strand options to be set to 0. * 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. * Samplevis 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. * Fixed a glitch where clicking the 'Truncate sequences to' label would select the marker spacing input. * 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. * 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. * 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. * 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. * Updated bundled D3 to v3.5.17. * Updated bundled Vega to v2.6.0.
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- 22 Mar, 2016 2 commits
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Hoogenboom, Jerry authored
* Added Noise column to the allele tables. * Added number of reads before correction to the allele tables. * Added raw numbers of reads to the Correction and Recovery columns of the allele tables. * Fixed issue with Samplevis HTML visualisations in Firefox and Internet Explorer that caused an uncessesary horizontal scroll bar in the options panel.
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Hoogenboom, Jerry authored
Changed: * The PctRecovery as used for automatic allele selection in Samplevis HTML visualisations as well as Samplestats is now computed w.r.t. the number of reads after correction, instead of the number of reads before correction. Added: * Added X_recovery columns to the output of the Samplestats tool. The value is equal to X_add / X_corrected * 100.
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- 21 Mar, 2016 1 commit
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Hoogenboom, Jerry authored
Fixed: * Fixed a glitch in Samplevis HTML visualisations, where it would fail to correctly maintain the user-(de)selected alleles when switching Split Markers on or off. Removed: * Removed -L/--check-length option from the TSSV tool, because it had no effect. Instead, the TSSV tool will always enforce the expected allele lengths specified in the library file. Behaviour has not changed.
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- 14 Mar, 2016 1 commit
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Hoogenboom, Jerry authored
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- 10 Mar, 2016 1 commit
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Hoogenboom, Jerry authored
Fixed: * The -c/--stuttermark-column option of Allelefinder was not filtering out the non-ALLELE sequences as it was supposed to. (This issue was introduced in ce7f34fb, in which a bug was fixed that caused this option to filter all sequences, including the ones marked with ALLELE. So it turns out this option has been broken since 732e83ba.) Improved: * Allelefinder will no longer reject a marker based on the number of reads of 'Other sequences'. * Adjusted sequence alignment parameters for mtDNA sequences to produce allele names that more closely follow historical mtDNA mutation nomenclature.
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- 09 Mar, 2016 1 commit
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Hoogenboom, Jerry authored
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- 08 Mar, 2016 2 commits
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Hoogenboom, Jerry authored
* Turned all '0.1dev' tool version numbers to '1.0.0'. * Changed Stuttermark's version number from '1.5' to '1.5.0'. * Added version numbers to the visualisations. * Updated README.rst to include all tools, but removed the usage details of Stuttermark because it is highly impractical to include usage details for all tools in the README file. I'll leave that to the -h/--help option and the yet-to-write FDSTools User's Handbook.
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Hoogenboom, Jerry authored
FDSTools would sometimes produce suboptimal alignments. Most notably, it it would produce multiple smaller insertions/deletions when the difference between two sequences could be described by one larger insertion/deletion in combination with a base substitution. The latter description is often more biologically sound and also usually results in a shorter allele name. * Fixed a bug that sometimes caused FDSTools to choose an incorrect path through the alignment matrix, producing a suboptimal alignment. * Tweaked the alignment parameters to produce more meaningful results.
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- 07 Mar, 2016 1 commit
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Hoogenboom, Jerry authored
This was missing from commit 29fcc171
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- 01 Mar, 2016 1 commit
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Hoogenboom, Jerry authored
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- 29 Feb, 2016 3 commits
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Hoogenboom, Jerry authored
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Hoogenboom, Jerry authored
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Hoogenboom, Jerry authored
Added: * Added a new section expected_allele_length to the FDSTools library format. In this section, the minimum and (optionally) maximum allele length of each marker can be specified. * Added -L/--check-length option to the TSSV tool. If specified, the tool will use the expected_allele_length values to filter the results. * Samplevis can now truncate long allele names to a given number of characters (defaulting to 70). * Added an option to Samplestats to keep negatives when filtering (abs filter). Changed: * Renamed the --aggregate-below-minimum option of the TSSV tool to --aggregate-filtered. Improved: * Added an option to read_sample_data_file such that other code can request or require that the X_corrected columns are used. * Samplestats will now round to 4 or 5 significant digits if a value is above 1000 or 10000, respectively. * BGHomRaw will no longer round the forward, reverse, and total columns. * When generating mtDNA allele names, FDSTools will now try to avoid creating gaps in the alignment of the sequences against the reference. * Grouped the filtering options of the TSSV tool in its help text. * Cleaned up some leftover code for special sequence value handling (more specifically: code that expected ensure_sequence_format to return False for special sequence values, which it no longer does). * Cleaned up some dead legacy code in reduce_read_counts.
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- 25 Feb, 2016 1 commit
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Hoogenboom, Jerry authored
New tool findnewalleles: * Given a list of known sequences, this tool can go through sample data files to mark all sequences that are not on the list. Fixed: * BGHomRaw, BGEstimate, BGHomStats, Stuttermodel, and Blame did not ignore the 'Other sequences' and 'No data' values that may occur in the place of a sequence as they were supposed to. Improved: * BGHomRaw will now include the sample tag in the "Missing allele X of marker Y" error message. Changed: * The -F/--sequence-format argument from BGHomRaw now defaults to "raw". Visualisations: * Updated Vega to version 2.5.0. * The new version of Vega allowed the sorting to be fixed in Samplevis, Profilevis, BGRawvis, and Stuttermodelvis. * Samplevis: * The 'Other sequences' bars are now drawn with an outline only. * STR alleles are now sorted by allele length by default (this can be toggled with a checkbox in HTML visualisations, and with an option in the Vis tool). * Fixed the clipping of the start of long allele names when printing SVGs from Google Chrome. * Added a note (as '?' help tooltip) to the Common axis range option in the HTML visualisation, to inform the user of the fact that the Split markers option needs to be off for it to work.
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- 22 Feb, 2016 1 commit
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Hoogenboom, Jerry authored
Fixed: * Fixed crash in Samplestats. It would crash if BGCorrect columns were present. * Fixed glitch in Samplevis that allowed clicking the 'Other sequences' bars if the input data already contained the 'Other sequences' entry. Improved: * The TSSV tool will now drop any sequences that contain anything other than A, C, T, and G. If the -A option is given, these sequences will still be added to the marker aggregates. Many other tools will fail when confronted with such invalid sequences, especially when allele names need to be generated. * In Samplevis, the sequences are now consistently sorted (except for some inconsistency caused by a bug in Vega). The sorting is based on read counts and is the same as used for the allele tables in Samplevis HTML visualisations. * Added a comment line that mentions genome build GRCh38 and rCRS to the genome_position block in the libconvert output. This is mainly for documentation purposes; users are free to change this line if they use a different reference. * Minor styling changes to Samplevis HTML visualisations.
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- 15 Feb, 2016 1 commit
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Hoogenboom, Jerry authored
* Samplevis now features a responsive design. The options have been moved from the overlay into a menu bar that changes place and shape depending on the width and height of the viewport. * All option labels are now clickable. When clicked, the corresponding option receives focus. * The 'Save image', 'Save table', and 'Clear manually added/removed' links are now always visible, but change appearance when unavailable. * When a 'No data' line is found for one or more markers, a warning is displayed at the bottom of the screen. * Fixed bug that caused user-selected and user-removed alleles to get lost when the corresponding marker is filtered out using the marker name filter. * Fixed bug in the printing stylesheet that caused conforming browsers to break pages between the graph and the table of a marker, instead of avoiding to do so. * In HTML visualisations with embedded data, the name of the sample data file is now shown in the place of the file selection element. Other Samplevis fixes and improvements: * Added option to show sequences that are filtered from the graphs as a single 'Other sequences' aggregate entry per marker (default: on). * For alleles that end up at a negative read count after correction now have a strand balance line in the 'overlap' portion of their bar only. * The strand bias mark is now correctly positioned when using the square root scale. Improved: * HTML visualisations with embedded data will now use a proper filename for the 'Save graph' and 'Save table' options.
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- 04 Feb, 2016 2 commits
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Hoogenboom, Jerry authored
Fixed: * Fixed a javascript crash in Samplevis HTML Visualisations. * Converted two unexpected tab characters to spaces in README.rst. Improved: * Samplestats will now sort the output by marker name.
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Hoogenboom, Jerry authored
Improved: * Added -A/--aggregate-below-minimum option to the TSSV tool. This will add a line with 'Other sequences' to the output summing all sequences that were not reported because they had less reads than was specified with the -a/--minimum option. * Clarified the help text for the -D/--dir option of the TSSV tool. Fixed: * Updated all tools to consistently handle cases where 'No data' or 'Other sequences' occurs in place of a sequence.
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- 02 Feb, 2016 1 commit
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Hoogenboom, Jerry authored
Updated Stuttermark to v1.5. WARNING: This version of Stuttermark is INCOMPATIBLE with output from previous versions of FDSTools and TSSV. Introducing TSSV-Lite * New tool tssv acts as a wrapper around TSSV-Lite (tssvl). Its primary purpose is to allow running TSSV-Lite without having to convert the FDSTools library to TSSV format, and to offer allelename output. Like all other tools in FDSTools, it also works with TSSV library files but its allele name generation capabilities are limited in that case. Changed: * TSSV-Lite and the new TSSV tool in FDSTools have two columns renamed w.r.t. the original TSSV program: 'name' has been changed to 'marker', and 'allele' has been changed to 'sequence'. All tools in FDSTools have been updated to use the new column names. This change affects Allelefinder, BGCorrect, BGEstimate, BGHomRaw, BGHomStats, BGPredict, Blame, Samplestats, Samplevis, Stuttermark, Stuttermodel, and Seqconvert. Note that this change will BREAK COMPATIBILITY of these tools with old data files. Fixed: * In Samplevis HTML visualisations, the "percentage recovery" table filtering option used the absolute number of recovered reads instead. * Added PctRecovery to the tables in Samplevis HTML visualisations. * BGPredict will now print a nice error message if the -n/--min-pct option is set to zero or a negative number, to avoid division by zero. * Samplestats would crash if the input file contained the flags column. * FDSTools would crash when trying to convert sequences to allele names using a TSSV library. Improved: * Libconvert will no longer include duplicate sequences in the STR defenition when converting to TSSV format and the reference sequence of one of the markers is the same as one of its aliases, or when aliases of one marker share one or more prefix or suffix sequences. * Updated add_input_output_args() such that the output file is a positional argument (instead of -o) for tools that have a single input file and no support for batches. * Updated add_sequence_format_args() such that the library file can be made a required argument. * Refined the FDSTools package description, since FDSTools does more than just noise filteirng. * FDSTools will now do a marginally better job at producing allele names for sequences that do not exactly match the provided STR pattern. When seeking the longest matching portion of the sequence, it will now also test the reversed sequence with a reversed pattern, which sometimes yields a longer match. It is still not optimal, though, but some refactoring has been done to move away from regular expressions. * BGCorrect will now also fill in correction_flags for newly added sequences. * Adjusted the help text of Samplestats to include the fact that the -c and -y options have an OR relation instead of an AND relation. * BGCorrect, BGEstimate, BGHomRaw, BGHomStats, BGPredict, and Stuttermodel will now ignore special values that may appear in the place of a sequence (currently: 'Other sequences' and 'No data'). Removed: * The -m/--marker-column and -a/--allele-column arguments of BGPredict had no effect and have been removed. Visualisations: * Updated bundled D3 to v3.5.12. * In HTML visualisations, if the page is scrolled to the right edge when an option is changed that causes the graphs to become wider, the page now remains scrolled to the right. * Samplevis HTML visualisations: * Added 'Clear manually added/removed' link to the table filtering. * Reduced flicker of the mouse cursor in Internet Explorer. * Added 'Common axis range' checkbox (only available when 'Split markers' is off). * Added 'Save table' link to save the table of selected alleles to a tab-separated file. * Added 'PctRecovery' column to the tables of selected alleles. * An alert box is now shown when a data file is loaded that contains markers that have 'No data'. * Added 'Percentage of total reads' to the graph filtering options. * Added a note to the table filtering options to explain that the minimum percentage correction and recovery have an OR relation.
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- 18 Jan, 2016 1 commit
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Hoogenboom, Jerry authored
Fixed: * Fixed a crash in BGMerge. * Fixed bug in BGCorrect that resulted in incorrect values in the *_add and *_corrected columns (yes, you, 8685a304). * Fixed a glitch in BGCorrect that prevented it from ever writing corrected_bgestimate in the correction_flags column. Improved: * BGEstimate will now include the sample tag in the error messages for missing alleles and alleles with 0 reads. * Strand bias lines in Samplevis are now clamped to the 0-100% range. BGCorrect may cause forward read percentages outside this range. Visualisations: * Updated Vega to version 2.4.2. * Fixed drag-'n-drop behaviour for HTML visualisations in Internet Explorer and Firefox. * Fixed the Save Image link when viewing HTML visualisations in Internet Explorer 10 and above. * Added http-equiv="X-UA-Compatible" content="IE=edge" meta-tag to all visualisations to prevent Internet Explorer from entering quirks mode. * Samplevis: * Fixed glitch that would sometimes cause a second horizontal scroll bar to appear. * Graphs now render much more quickly when 'Split markers' is on, and Chrome no longer crashes on large sample files with this option set.
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- 09 Dec, 2015 1 commit
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Hoogenboom, Jerry authored
Fixed: * When converting STR allele names to sequences, FDSTools would reject any prefix variants with a false message stating that the variant does not match the reference sequence. * The Samplestats tool would not allow the -b/--min-per-strand option to be set to zero. Improved: * Moved the flags generated by BGCorrect to a new column named correction_flags. Some of the values have been renamed for clarity, and this column now always contains a value. * The Samplestats tool will no longer add the not_corrected flag to each sequence, as it does not add the correction_flags column. * The Samplestats tool now supports filtering sequences. For filtering, the same set of options is available as those used for marking alleles. The filtering options use upper case letters and have '-filt' appended to their long name. The new -a/--filter-action option defines what should be done with filtered sequencies. 'off', the default, disables filtering; 'combine' replaces filtered sequences with a new line containing aggregated data; 'delete' removes filtered sequences without leaving a trace. * The seqconvert tool is aware of the special 'Other sequences' value produced by Samplestats with -a/--filter-action set to 'combine'. Other tools will give an informative error message when the input contains this special value. * The Samplestats tool now accepts non-integer and negative numbers for -n/--min-reads and -b/--min-per-strand because after correction read counts are not necessarily nonnegative integers anymore. * The forward_correction and reverse_correction columns of Samplestats will now contain 0 if the sequence had exactly 0 reads both before and after correction (previously, this was -100). * Renamed the _mp columns of Samplestats to _mp_sum ("per-marker percentage of the sum") and introduced _mp_max columns ("per-marker percentage of the maximum"). * Samplestats and Samplevis HTML visualisations will now mark a sequence as 'allele' if the minimum amount of correction OR the minimum number of recovered reads is reached (as opposed to AND). This allows alleles on stutter positions to be detected. Changed: * The -r/--min-recovery option of Samplestats has been renamed to -y/--min-recovery, analogous to the new -Y/--min-recovery-filt. Visualisations: * Updated Vega to version 2.4.1. * Replaced the regular expression-based filters in all visualisations with a much simpler syntax. The new syntax uses space-separated search terms, defaulting to a 'contains'-type search method. If any search term is preceded by an equals sign, that term must be matched exactly. (The search terms themselves are actually still matched as regexes!) * Added 'show negative alleles' option (default on) to Samplevis. When enabled, the graph filtering options work on abs(value) instead of the value itself. * When sorting alleles in Samplevis, the allele name is now used as the final tiebreaker instead of the primary sorting column. * HTML visualisations no longer re-render the entire graph when changing the width. The same holds true for the height setting of Allelevis. * The tables in Samplevis HTML visualisations will now contain the information from BGCorrect's correction_flags column in the Notes column.
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- 03 Dec, 2015 1 commit
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Hoogenboom, Jerry authored
Fixed: * In Samplevis HTML visualisations, the automatic allele selection was only checking the number of reverse reads for the 'minimum number of reads per orientation' setting. * In Samplevis HTML visualisations, automatic allele selection would fail to select alleles that had exactly the given minimum number of reads. * FDSTools would sometimes calculate incorrect and even negative repeat counts when producing TSSV-style sequences and allele names for sequences that did not exactly fit the STR structure given in the library. Improved: * The Samplestats tool now offers the same possibilities to mark alleles as Samplevis HTML visualisations do. * In Samplevis HTML visualisations, user-removed alleles now have a line through their table row. * Added a reference to https://docs.python.org/howto/regex in the sample tag parsing options section of the help text of many tools. * FDSTools will now do a better job of finding the longest possible match of the STR repeat definition to produce TSSV-style sequences and allele names for seqences that do not exactly fit the STR structure given in the library. Added: * New visualisation type 'allele'. With Allelevis, you can generate a graph of the alleles of the reference samples (output from Allelefinder). (Known bug: it has a 'funny' amount of padding.)
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- 01 Dec, 2015 1 commit
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Hoogenboom, Jerry authored
Fixed: * The Vis tool no longer crashes if you specify '-' as the input file without piping data in from another program. It will just produce a visualisation file with no embedded data instead. * FDSTools would crash when generating an allele name for a sequence of an STR marker that contained the prefix and suffix of the marker but not the actual STR (yes, this happened). * Stuttermodelvis would draw all 'All data' fits in the graphs of all repeat unit sequences, instead of just the 'All data' fit that was fitted to the data of a particular repeat sequence. Improved: * BGHomStats, BGHomRaw, and Samplestats now round their output to three significant digits. * BGCorrect now rounds its output to 3 decimal positions. Various enhancements to Samplevis HTML visualisations: * Added a whole new set of options which are used to automatically select the true alleles in a sample. * Added an option to split the graphs and the table up per marker. * The selected alleles are no longer lost when the graphs are re-rendered due to changed options. * Added some more columns to the table of selected alleles and made the table prettier. * Added a dedicated stylesheet for printing, which transforms the web page into a nicely formatted report when printed. * Option groups can now be hidden separately. * Filtering options are now based on the read numbers after correction. * The mouse cursor now changes to a 'pointer' style cursor (usually a hand with stretched index finger) when hovered over the clickable portion of the graph. Visualisations: * Updated Vega to version 2.4.0 and d3 to version 3.5.10. * All visualisations now use signals to set the options. This allows them to be updated without re-parsing the entire graph spec in most cases, which is much faster. * Using new cross-and-filter capabilities in bgrawvis, profilevis, samplevis, and stuttermodelvis. This greatly reduces Vega's memory usage and speeds up rendering. * The name of the currently loaded data file is prepended to the page title in HTML visualisations. * If a file is loaded into an HTML visualisation by drag-and-drop, the name of the loaded file is displayed on the file input element. * A new -T/--title option for the Vis tool allows for specifying something that should be prepended to the page title of HTML visualisations. This is particularly useful when data is piped in, because no file name is available in that case. * Asynchronous rendering of visualisations is now cancelled if a new asynchronous rendering task has already been scheduled (HTML visualisations only).
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- 23 Nov, 2015 1 commit
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Hoogenboom, Jerry authored
* New tool Samplestats computes various sequence-centric statistics for sample data files. Most statistics relate to correction amounts and are thus only included if the input file contains BGCorrect columns. * The starting position can now be ommitted from the [genome_position] in FDSTools library files. A default value of 1 will be used in this case. * The setup.py script can now also be run without explicitly specifying Python as the interpreter (it now has a shebang line).
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- 16 Nov, 2015 2 commits
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Hoogenboom, Jerry authored
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Hoogenboom, Jerry authored
Fixed: * The 'to' base in variants called on mtDNA was incorrect. This bug could also cause FDSTools to crash. * FDSTools would crash if you tried to generate an allele name for a primer dimer of an mtDNA marker. (Now, you get an insane but entirely accurate allele name instead.) * Fixed bug that caused some perfectly valid mtDNA allele names to be rejected when attempting to convert them back to raw sequences. Improved: * You can now also specify the ending position of the markers in the FDSTools library. If you do, you may also additionally specify a second start position (and optionally also a second end position, and so on). FDSTools will interpret this as that the marker is the concatenation of each of these fragments. This was primarily introduced to support mtDNA fragments that contain (somewhere in the middle) the origin of mtDNA base numbering. * More helpful error message when format violations are detected while parsing the library file. * More helpful error message when the -e/--tag-expr regular expression could not be compiled. * Added a paragraph about sequence alignment caching to the help text of Seqconvert. * Added a 'flags' column to BGCorrect output, which gives information about the data that was used to do the correction. Background noise profiles: * Removed -C/--cross-tabular option from BGEstimate, BGPredict, and BGMerge and also removed the ability to read files in this format. * BGEstimate, BGHomStats, and BGPredict now add a column 'tool' with their name to the output.
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- 05 Nov, 2015 1 commit
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Hoogenboom, Jerry authored
* The legend items now have more descriptive names and also include the strand balance line. * Added 5% to the X axis scale, to reassure people that they are really seeing the entire bar. * The X axis scale limits are now rounded to a 'nice' number and includes a label for its ending tick mark. * Added filter for a minimum number of reads per orientation. * Strand bias line now becomes red if less than a certain percentage (default 25) of reads is on one strand, and a star is placed at the end of the allele's bar. * Alleles can be selected (and deselectd) by clicking them (HTML only). * Selected alleles appear with a green italic allele name. * Data for selected alleles is summarised in a table at the bottom of the page. This is WIP and currently only includes the read total.
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- 04 Nov, 2015 1 commit
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Hoogenboom, Jerry authored
Additions and improvements to the FDSTools library file format: * New [genome_position] section in FDSTools-style library files allows for specifying the chromosome and position of each marker. * New [no_repeat] section in FDSTools-style library files allows for including non-STR markers. * Comma/semicolon/space-separated values in FDSTools-style library files can now also be separated by tab characters and multiple consecutive separators are no longer collapsed (with the exception of whitespace). * If no prefix and/or suffix has been specified for an alias, the prefix/suffix of the marker itself is used. * Implemented support for non-STR markers (e.g. SNP clusters) and mtDNA markers. Allele names of the latter follow mtDNA nomenclature. * Improved the logic of generating STR allele names for sequences that have a prefix or suffix sequence that was not included in the library file. * Updated and clarified various explanatory texts in generated FDSTools library files. Fixed: * Fixed a bug that caused prefix/suffix variants in aliases to go missing in allele names. Improved file handling: * Library files are now closed immediately after parsing them. * Sample data input files are opened one at a time now. Visualisations: * Updated Vega to version 2.3.1. * Worked around a bug in Google Chrome that caused the 'Save image' link to stop working after having been used once.
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- 22 Sep, 2015 1 commit
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jhoogenboom authored
Will complete this when updating to Vega 2.2.5 or newer, which contains a new feature that I contributed specifically for this.
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- 10 Sep, 2015 1 commit
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jhoogenboom authored
* Properly implemented the options on the StuttermodelVis HTML visualisation. * Added filtering options for marker and repeat unit to StuttermodelVis. * Added StuttermodelVis to the Vis tool. General visualisation changes: * Updated Vega to v2.2.4. * Fixed glitch that caused mouseover events in HTML visualisations to stop working after the renderer was switched. * The file name suggested by the Save Image link in HTML visualisations is now derived from the name of the loaded data file.
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- 04 Sep, 2015 1 commit
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jhoogenboom authored
And thereby removed a dirty workaround for a bug I found.
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- 03 Sep, 2015 1 commit
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jhoogenboom authored
* Added StuttermodelVis HTML file and JSON spec. The rendering works, but some of the options are not implemented yet. It is also not yet added to the Vis tool. * Changed the order of stuttermodel's coefficients: 'a' used to be the most significant coefficient, now it is the least significant coefficient (the shift). The benefit of this is that when moving to higher-order polynomials, the extra coefficients do not change the meaning of the others. So 'a' is now always the shift, 'b' is the linear component, 'c' the quadratic, etc. * Added some development notes (including todo list) that I had kept outside of the project until now.
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- 01 Sep, 2015 2 commits
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jhoogenboom authored
* BGCorrect and Stuttermark will now exit with an error message if more than one input file for the same sample is specified and no separate output files are given. Previously these tools would just overwrite the output file repeatedly, discarding the output of all but the last data file of the sample. * Removed to main() functions and related stubs from the tools because they are not actually runnable directly anyway. * Added some more help text to some of the tools. * Doubled the size of the marker name filter input element on the HTML visualisations.
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jhoogenboom authored
Fixed: * Fixed crash that would occur when an empty sequence (primer dimer) is converted from raw to TSSV-style (or allelename) format. * Fixed bug in BGHomRaw that caused incorrect sample tags in the output. * Fixed bug that caused allele names with negative CE numbers and names of primer dimers to be regarded as 'invalid allele names' even though FDSTools generated those names itself. * Fixed crash when reading sample data while looking for an annotation column. * Fixed bug in Allelefinder resulting in the complete absence of output that occurred when a column name with Stuttermark output was specified. Changed: * Restyled the Options box on HTML visualisations. It is now less transparent and oriented more vertically to reduce overlap with the visualisation. Options are now presented in groups. * Updated Vega to version 2.2.1. New: * Added *_corrected columns to BGCorrect output for convenience. E.g., the total_corrected column contains the value of total-total_noise+total_add. * Added -L/--log-scale option to the Vis tool.
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