- 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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- 01 Sep, 2015 1 commit
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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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- 12 Aug, 2015 1 commit
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jhoogenboom authored
* New tool BGMerge can be used to merge background noise profiles (e.g., merge BGPredict output with a database previously obtained from BGEstimate). * Fixed two major bugs in BGPredict that resulted in incorrect fit functions being used. * BGEstimate, BGPredict, BGHomStats, Blame, and StutterModel no longer crash if a library file is specified. * Added reverse strand profile estimation to BGPredict.
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