Known bad alignment - #828
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Old version does not discriminate between raw and all in select_transcripts field. This does not match VV anf VF processing and leads to slower responses when only latest transcript versions are required. Now, raw returns all transcripts at all versions and all returns all transcripts at latest versions. Closes issue #804
Certain alignments are too bad to justify keeping. The list in the file transcript_map_data.py can be used to filter mapping options, even if VVTA is updated and new rogue alignments are identified.
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Looks OK, just a question on the Suffixes, and a possible simplification. I would just hit approve but I think that the suffix issue needs thinking on at least first. I do wonder about doing a latest transcripts only materialised view for VVTA, but how to deal with the differing (suffixed) Ensembl data is a fun question, and we would then need to plumb it in correctly later in multiple places. |
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will fix this up, but I have a feeling that there are other instances in VV and VF where we need to fix too |
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I believe that the intention was to just not use them for normal output, mostly, but to keep them to have them to map from if user input matched, with appropriate warnings, if we wanted to handle this later. But we never did get to being able to handle that. Not only as the ID for the user input would not match the ID for the ensemble data, so in that case so we would have to check specifically for this issue, but also because we would then have to handle the possible inputs interpretations for GRCh37/38 and make sure they pass through the rest of the code properly. As such we probably just need to make sure nothing is crashing, for now, since this would be bonus feature development, not bug-fixing. I think the intention was that if we got around to this to find both suffixed and resubmit the 2 suffixed with warnings?, e.g |
Ensembl transcripts with the same ID but requiring genome build info require additional handling
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hope this push maintains the required format. We will add the other stuff to the ever expandin to do list :) |
hdp.get_tx_for_gene has specific structures that need to be filtered out. This can be plugged into all other uses of hdp.get_tx_for_gene and adapted for other similar lists from hdp
Allows the API to optionally set the shorthand vcf format with a mod to the interface. The gui will keep the toggle switched on i.e. True. Also, range increased to 500 to allow capture or pretty much all vars in dbSNP
John-F-Wagstaff
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Looks good now if you want to push it.
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