git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@573 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/rpclib-branch@535 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@527 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

This fixes Trac bug #95.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@524 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Until now, the name checker form used POST requests. As a special case for
linking from LOVD, GET requests were handled by showing results without the
full interface (header, menu, etc). Ordinary linking was done to a separate
checkForward location which then set a cookie with the variant name and a
redirect to the name checker results. This was all very hackish and somewhat
broken (see Track issue #94).

This commit refactors the name checker to use GET requests, so ordinary
bookmarking of result pages is possible. All old entrypoints are handled with
a redirect for backwards compatibility.

Worth mentioning is that variant descriptions in the name checker are now
limited in length by the maximum query string length. However, this maximum
is several thousand characters with Internet Explorer having the lowest
maximum of just over 2000. Longer descriptions are not practically checked
with the name checker web interface anyway, so this should not be a problem.


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For UD slices we also generate g. descriptions on the chromosome reference. We
now also apply the roll rule there and use correct ranges and sequences on the
reverse strand. Fixes #75.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@495 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

During import of the NCBI transcript mappings, CDS start or stop positions
were not picked up for some transcripts (where these are on exon boundaries).

Bug reported by S Venkata Suresh Kumar.


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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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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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Fixes #74.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@410 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1