• Hoogenboom, Jerry's avatar
    Various fixes and improvements · 313867bc
    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.
    313867bc
notes.txt 7.78 KB