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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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Committing partway through removing a bunch of unused code/files just in case something necessary gets removed
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Improved the "scatterplot matrix" feature on the trait page so that
it matches the chosen trait against every selected trait
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adding the correlation matrix page
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Fixed one genofile that had extra quotation marks
in the comments that caused an error
Defaults mb_graph_interval to 1 for species without chromosome
lengths in megabases
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Added option to limit results based on lod score (which also
changes the y-axis of the plot)
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chromosome-related attributes
Began to try and pass qtlreaper results as js_data to use when
drawing graphs
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Added a couple utility functions to the Chromosomes class in species.py
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in species.py
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Converted html for the mapping tabs to bootstrap and redid html inside of
the Interval Mapping tab
Added text input for # of permutation tests and bootstrap tests
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