Big update: Bumped version to v0.0.3
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.