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using precomputed kinship matrix
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drawing SNP density chart when results exceed a certain value, plus a couple minor fixes
Changed the header bar to put a few items under the "Help" option, since previously the header was too long and would go to a second line when the browser window width was smaller
Changed dataset info link on trait page to same as one on search page
Changed the mapping default to non-LOCO for the time being, until it is faster
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chart if results exceed some number (5000 on GN1)
- Removed unnecessary options from the mode bar for the trait page Plotly figures and changed the default to highlight points the mouse is hovering over
- Changed some file/function names related to mapping, which previously were erroneously named "marker_regression"
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Forgot to add to change user to root during the last commit
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Since I know I'll forget otherwise, updated instructions on starting up ES
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reference to probeSetSearch wasn't removed
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- Added all current SNP browser code (not complete yet)
- Added change to convert_geno_to_bimbam that makes it ignore .geno files marked as "filler" (so ones where the .geno file is fake and we sometimes directly receive the genotypes as BIMBAM)
- Changes TheSpecies object in species.py to accept species name as well as dataset name
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just clicking their row in collection
- Cofactor color picker now works in Safari/Macs
- Displays N for relevant samples in trait page sample table
- Don't show bar chart when N>256
- Mapping loading page contents better centered
- Anonymous collections timeout correctly listed as 30 days now
- Minor allele frequency can actually be changed for GEMMA now (previously didn't work)
- Fixed transcript position marker location for mapping results
- Notifies user if their e-mail isn't associated with an account when they attempt to request forgotten password
- Users can now map with submitted traits
- Histogram width changes depending upon number of bins (need to improve this still)
- Improved Q-q plot (previously called "probability plot")
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Gemma optimized for production
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Added "change user to elasticsearch" to the description of how to start elasticsearch
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Added Phenogen track to mapping results
Added comparison bar chart figure
Simplified global search to not build trait/dataset objects, which speeds thing up considerably
Fixed correlation matrix to correctly deal with 0 values
Fixed issue where anonymous collections couldn't be created if none already existed
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I added the command to start elasticsearch, since I've had to look it up/ask Pjotr about it a couple times now.
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Figures now correctly rescale when transforms are applied
Fixed height of probability plot
Removed some text related to pylmm since it's currently not being used
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trait page
Got figures mostly working with transformed values, except for changing the y-axis range of one
Fixed issue with the home page "Make Default" button position (as well as the drop-downs in general)
Added timeout to Elasticsearch connection to fix related error
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previously
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should have their full functionality back (adding/removing collections, adding/removing traits, etc)
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staging, though still not sure why it's working on production without that change
Added script to convert the dryad format genotype files to BIMBAM
removed db_uri from parameters of parse_db_uri in gen_select_dataset.py, since it can now just pull it from settings as a global variable
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sample data into ElasticSearch
Added option to replace trait page sample/strain values with normalized ones
Began editing Lei's scatterplot code
Changed elasticsearch_tools' get_elasticsearch_connection so that it can also be used for purposes other than user authentication (by adding a "for_user" parameter)
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Fixed issue where GEMMA + LOCO wasn't working with AIL (and probably some other groups)
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instead of -lmm 1 (Wald test)
Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py)
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set width
Changed to using BIMBAM files to build Marker objects in dataset.py
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some problem. Probably better to leave this file alone for the time being.
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Removed some unused code from the other files listed
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marker_regression_gn1.py
marker_regression.py
do_search.py
export_traits.py
heatmap.py
GeneUtil.py
heatmap.html
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Testing
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testing
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Testing
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* I can't swear on this, but it seems the presence of these statements
was causing elasticsearch to act weird.
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* Update the indexes mappings to be compatible with the newer
Elasticsearch 6.2.* series.
Close the index before updating it, and reopen it after to help with
the re-indexing of the data.
* Update the error logger to include the exception that was thrown.
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* Prevent elasticsearch from analysing and tokenising the email_address
field so as to avoid issue with getting back all email addresses with
the same domain as the one being searched for.
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