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- Fixed the bug in the insertions / duplications code.
- Added documentation and pointers on how to integrate this as a module.
- Added a wrapper for the recursive function.



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Some genes (e.g. in the PAR) are mapped on both the X and Y chromosomes, but
are (apart from the chromosome names) indistinguishable from transcripts that
are mapped using different contigs. Transcripts of the latter type should be
merged, those of the former type should not be merged.

Our fix consists of only including exons where positions are consistent with
the transcript mapping and allowing transcripts to be mapped more than once,
but only to two different chromosomes.

This fixes #82.


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  description of the stored raw variant.
- Made a function that returns an allele description given a list of raw
  variants.
- Removed the hgvs member variable from RawVar().
- Removed the HGVS description generation from DNA_description().
- Started refacoring the DNA_description() function.

TODO: rolling for insertions and duplications is not working properly.



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as a list of objects.


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For use by LOVD (NGS variants import, Jerry Hoogenboom), implement the SOAP
webservice method getTranscriptsMapping. The calling signature is the same as
for the existing getTranscriptsRange method, but the new method returns more
than just the transcript names.


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  the length of the longest common substring in two sequences.
- Changed the splitting on the longest common substring for direct slicing
  based on the new return values of LongestCommonSubstring().
- Added the removal of the lcs from the leftVariant and the lcp from the
  rightVariant in the inversion part of the DNA_description() function.


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sequences.



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Previously, the 'color' field in the BED track we provide for the Genome
Browser was set to the empty string, but Gerard informed us that this is not
(always) handled correctly:

   Expecting number field 5 line 2 of https://mutalyzer.nl/bed?..., got +

We now explicitely set the 'color' field to '0'.


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the product list. Please check this fix.

Made some trivial changes in the rest of the files.


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