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- Nov 22, 2013
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Arnaud Kerhornou authored
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Arnaud Kerhornou authored
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Arnaud Kerhornou authored
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Arnaud Kerhornou authored
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Arnaud Kerhornou authored
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- Nov 18, 2013
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Magali Ruffier authored
stable id lookup now also contains an archive_id_lookup table, which stores retired stable ids also reduced the required memory for release 74 and 66 species, it ran with less than 600Mb, no need to request 1.5G
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- Nov 15, 2013
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Andy Yates authored
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Andy Yates authored
switch to using the local as default. otherwise we cannot have a test passing until we have committed to version control
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Andy Yates authored
switch to using ENV variables. Otherwise we run the risk of not being able to run the tests in any kind of test harness tool
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Andy Yates authored
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Andy Yates authored
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Andy Yates authored
A number of params are missing their - flag. That means the new XS rearrange does not work (it is a bug not a feature)
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Andy Yates authored
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Andy Yates authored
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- Nov 14, 2013
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Arnaud Kerhornou authored
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Arnaud Kerhornou authored
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Arnaud Kerhornou authored
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- Nov 12, 2013
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Alessandro Vullo authored
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Alessandro Vullo authored
- schema version change: 74 --> 75 - addition of source column to transcript table.
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Alessandro Vullo authored
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Andy Yates authored
Our lookups of primary accessions and display labels with the Xref table was flawed. Seems MySQL can only use 1 index per query and it is not possible to create a single index that can handle querying on two columns when either could be our matching value. Solution is to break the query into two parts each targetting a single column. MySQL is a lot happier about this and query times have dropped from 30 seconds on USEast to 18ms (9ms per query).
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Alessandro Vullo authored
When a feature is returned by a method in its coordinate system (e.g. fetch_by_dbID) and it's on a circular chromosome and spans the origin of replication, Mapper::add_map_coordinates aborts since it's testing the length of the contig against the difference between chr_end and chr_start.
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- Nov 11, 2013
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Magali Ruffier authored
same as store_mapping_path, but for multiple mappings a multiple mapping is needed when a single component can be mapped to multiple assembled regions this uses the '#' operator instead of the '|' for the mapping key
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Magali Ruffier authored
requires a number of updates to methods when adding/fetching mapping_path methods used to create mapping_keys as name1:version1|name2:version2 if there is no version, do not add ':' either for add_mapping_path method, do not sort list of coord systems by rank first argument is the assembled, second argument is the component, regardless of rank
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Magali Ruffier authored
also, when adding_mapping_path, do not expect the method to order coord systems by rank, it will use the first argument as assembled, the second argument as component
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Magali Ruffier authored
works similar to store_assembly, used to check if assembly entry already exists between 2 slices before attempting to store also corrected typo in store_assembly method, table used is assembly, not analysis
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- Nov 08, 2013
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Magali Ruffier authored
uses code to fetch result
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- Nov 07, 2013
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Alessandro Vullo authored
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- Nov 05, 2013
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Laurent Gil authored
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- Oct 31, 2013
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Alessandro Vullo authored
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Alessandro Vullo authored
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- Oct 30, 2013
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Andy Yates authored
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Andy Yates authored
The ID for simple features seem to be poorly defined and repetitive. Better to supress for the sake of GFF3.
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- Oct 29, 2013
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Alessandro Vullo authored
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Alessandro Vullo authored
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- Oct 25, 2013
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Alessandro Vullo authored
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- Oct 24, 2013
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Dan Sheppard authored
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Dan Sheppard authored
readable format for pipelines, etc.
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- Oct 23, 2013
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Dan Sheppard authored
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Andy Yates authored
The idea is good. Consult multiple adaptors as if they are one logical adaptor with the same query. Thing is that the old version was abused. Let's stop that now and bring in this nicer new version which does work well
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