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2016-04-20[PATCH 042/100] Sanitizing locationsPjotr Prins
2016-04-20[PATCH 041/100] Fixes for running toolsPjotr Prins
2016-04-20When a sample does not exist we should not set sample_data to None. Better ↵pjotrp
to leave it out so it never gets processed again.
2016-04-20-aPjotr Prins
[PATCH 039/100] Removing commented code
2016-04-20-aPjotr Prins
[PATCH 038/100] Fix compile errors
2016-04-20[PATCH 037/100] WebQtlConfig: sanitizing naming and used varsPjotr Prins
2016-04-20Settled on the _COMMAND syntax over _RUNpjotrp
2016-04-20With missing samples to not add them to the result setpjotrp
2016-04-20This threw an error when sample is missing in the DB.pjotrp
Let sample pass without data if the sample/genotype does not exist in the database.
2016-04-20[PATCH 033/100] Refactored file searchingPjotr Prins
2016-04-20[PATCH 032/100] file locating: error checking is built-inPjotr Prins
2016-04-20Fine tuning file locatingpjotrp
2016-04-20tools.py: add function locate_without_errorpjotrp
2016-04-20[PATCH 027/100] Introduce tools.locatePjotr Prins
2016-04-20[PATCH 026/100] Introducing cached values PYLMM_COMMAND,Pjotr Prins
GEMMA_COMMAND, PLINK_COMMAND and TEMPDIR
2016-04-20Introducing TEMPDIRpjotrp
2016-04-20[PATCH 024/100] Sanitizing file handlingPjotr Prins
2016-04-20[PATCH 023/100] WIP fixing all pathsPjotr Prins
2016-04-20Remover dependency to logger_tree (may reintroduce later)pjotrp
2016-04-20[PATCH 018/100] Find external tools: refactored code to work with GNU GuixPjotr Prins
2016-04-20Removed import htmlgen as is not used (apparently)pjotrp
2016-04-18Additive effect lines are now separated by chromosome (like the qtl line in ↵zsloan
the last commit) Fixed order of stats table in trait page Removed the qtl results table from chromosome view; will add the Interval Analyst output later
2016-04-14Fixed issue where qtl lines in interval mapping wouldn't connect between ↵zsloan
chromosomes Added text explaining what * indicates in the mapping options menu Removed ranges (log2 and fold) from stats table for phenotype traits
2016-04-13Moved the code getting the description/location because it was throwing an ↵zsloan
error for phenotype traits
2016-04-13Global search should be able to return description and location columns nowzsloan
2016-04-11Changed the way trait data is retrieved for the global search page (it now ↵zsloan
gets the LRS location repr and other variables needed to display in table during the retrieve_info function in trait.py instead of retrieve_trait_info in dataset.py) This change increases the speed by a bit (85 seconds to 66 seconds for example) Made the column width for location a bit wider for global search page so it doesn't spill onto a second line
2016-04-07Added option to change the maximum y-axis value for GN1 mapping figurezsloan
2016-04-07Permutation figure and x-axis label should change to correctly reflect the ↵zsloan
mapping scale (lrs or lod) Fixed bug where broken image link would appear if you ran R/qtl with no permutations
2016-04-07SNP Track option should now work for GN1 mapping figurezsloan
Fixed typo in show_trait html that caused the p-value slider to not work for correlations
2016-04-06The option to switch between LRS and LOD for the GN1 mapping figure should ↵zsloan
now work correctly. The correct value (LRS or LOD) will now be displayed in the results table Added glossary links for GN1 mapping figure options (permutations, bootstrap, etc)
2016-04-06Setting lodm to always be 1.0 fixes the issue where it would incorrectly ↵zsloan
display LOD scores for the Y-Axis instead of LRS values
2016-04-06Permutations (suggestive/significant lines, legend, and histogram) should ↵zsloan
now work for both R/qtl and qtl reaper mapping. Changed the logic for receiving permutation/bootstrap info when loading mapping page in different ways (from show_trait, from remapping, from clicking single chromosome) Added text below figure when Allele Effects selected/relevant
2016-04-05Bootstrap test should now work correctly for qtl reaper mapping method on ↵zsloan
full genome view There seems to be some issue with the way it does single chromosome bootstrap tests compared with GN1, though. It seems like GN1 completely re-runs the test for that specific chromosome, while GN2 just takes a subset from the previously calculated bootstraps
2016-04-05Fixed issue where haplotype analyst option would appear when using ↵zsloan
genetic(centimorgan) mapping
2016-03-30Disabled Haplotype Analyst option if mapping scale is centimorgan/geneticzsloan
2016-03-30GN1 mapping now when mapping scale is centimorgan (for R/qtl)zsloan
Fixed some issues related to zooming in on chromosome X Fixed problem where it threw an error for mapping methods that didn't return additive effect Fixed problem where the endMb in the top form would be set to the endMb of the last chromosome when viewing full genome
2016-03-29Additive effect option now works for GN1 mapping figurezsloan
2016-03-29Forgot to add GeneralObject file needed for haplotype analyst in last commitzsloan
2016-03-29Haplotype Analyst now works for GN1 mapping figurezsloan
Chromosome drop-down select and Mb range text fields now are set to the values the user last selected
2016-03-28Legend option now works for GN1 mapping figurezsloan
2016-03-28Trait sample data table width now dynamically changes with number of ↵zsloan
attributes and standard error
2016-03-24Graph width can now be set in Mapping Resultszsloan
2016-03-24Add the Gene Track option to display the Gene Band for single chromosome viewzsloan
Fixed an issue where width wasn't being set correctly, so chromosome view is correct width now (was too short before)
2016-03-24Mapping results table is now limited to the top 200 markers; previously the ↵zsloan
page took a long time to load when there were too many markers
2016-03-23You can now select chromosome and an Mb range from the top menu and remapzsloan
The track in the single chromosome view to zoom into smaller intervals now works correctly again
2016-03-23Fixed GN1 mapping plots so that Y axis and the Y coordinates of manhattan ↵zsloan
plot points are correct Table filters markers so it can always be displayed now (previously was too large for GEMMA)
2016-03-21Manhattan plot option now works for GN1 map, and GEMMA is set to display as ↵zsloan
manhattan plot
2016-03-21Changed code parsing marker csv file to increase GEMMA speedzsloan
Currently commenting out the vector map/table for GEMMA since they cause the page to hang, I'll try to figure out a way to prevent this
2016-03-18Forgot to not retrieve sample data for the phenotype global search with the ↵zsloan
last commit, added it now
2016-03-18Replaced header with other information in qtl mapzsloan
Began adding menu to qtl map Fixed global search to not retrieve samples (to increase speed) Got the vector plot working again so it can be displayed alongside the gn1-style plot Only display the vector plot when doing GEMMA to speed up (this might not be necessary)