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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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