• Hoogenboom, Jerry's avatar
    Bug fixes and improvements in allele name gen and auto allele selection · 7820cad0
    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.)
    7820cad0
notes.txt 7.79 KB