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updates
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more issues to resolve, like setting initial column width
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Made changes to the tables of correlation results, collections, and search results:
- Added resizeable columns to correlation results and collections, but not to search results
because it seems that it requires Y scrolling to be set (I'll check if it makes sense to add scrolling
to the search results)
- Correlation results and collections are now in scrolling tables
- The style is the same across all of these tables now
Remaining issues:
- It doesn't seem like I can set the column width when initializing dataTables in
correlation results. I don't know why this is; it might be due to the table already being the size
of a full page. I want to be able to default to some good widths, even if the user can resize them
- I tried adding hoverForMore, but it doesn't seem to cooperate with datatable cells; I think this is
due to having to put the text in a div.
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On branch master
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Conflicts:
wqflask/wqflask/templates/search_result_page.html
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On branch master
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incorrectly converted to json
Fixed GO search to work with combined searches
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Fixed several issues with existing searches; for example, the user can type "Chr" before the chromosome parameter (for example LRS=(9 999 Chr2 100 105) )
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appearing for human groups
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Currently we still usually get our samplelists from the genofile. This is
dumb because it results in us having a bunch of "dummy" genofiles for certain
data sets (seems to be mostly human ones). This means that checking for the
genofile alone isn't enough to determine if a mapping method should exist
for a given group
I wrote some code that will instead get the samplelist from the plink .fam file
for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy
.geno files, but we can't yet do so because it's currently the only place we seem to be storing
the sample list for some groups.
I also moved gemma into the plink directory to get it out of the git tree.
Since it uses the same files as plink, it doesn't make sense for it
to be in its own separate directory
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trait.py. Since I couldn't find the purpose of the assert statement I removed it.
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instead of getting an Internal Server Error
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and trans combined searches
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combined searches
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Fixes #69
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SQL security fixes
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results were displayed.
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due to a chromosome (in this case the last) not having any markers.
Improved the way plink gets its path/command to use a method similar to the
one Pjotr used with pylmm. I'll also do this for the other mapping methods.
Fixed issue where the Y axis would always say LOD score. It now says LRS for
mapping methods that return LRS
Switched interval mapping (qtl reaper) to use the marker_regression template and removed the interval_mapping template (since it's unnecessary)
Some commented out changes remain (in show_trait_mapping_tools and create_lodchart) from when I was attempting to open the mapping results
in a new page. I had resolved every issue but the mapping javascript (lod_chart) not
being able to access js_data (which has all the result data; markers, p-values, etc). I'm pretty
sure that this is because js_data was inserted into the html after the page was loaded while
the chart code ran immediately. I experimented with adding a short timeout to the mapping
javascript and data table javascript, but while it worked for the table it did not work for the
mapping figure. I don't know why this is.
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Conflicts:
wqflask/wqflask/templates/marker_regression.html
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fix genotype search
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Also changed to where results open in new window instead of colorbox, though an issue remains where the css doesn't seem to be getting imported properly.
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move duplicated code into a method,
handle the case of missing f1/f12 correctly
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