Display genotypes for a single variant in it's own column

[Nicklas Nordborg]

The use case is that we have a list of a handful of variants that we want to get the genotype for all samples as a table matrix. It is possible to do it one by one and then merge together the results, but it is a bit complicated since not all results may contain all samples.

It would be nice to have a function were a user can select a variant from a query and say "Display the genotype for this variant in a separate column". The columns should be filterable and exportable and it should be possible to do this for multiple variants at the same time.

[Nicklas Nordborg]

In 7740:

References #1596: Display genotypes for a single variant in it's own column

Started to implement this functionality. It is intended to be generic but is currently only working for the Oncoarray index.

Filtering has not yet been implemented.

[Nicklas Nordborg]

In 7741:

References #1596: Display genotypes for a single variant in it's own column

Implemented support for filtering on the Oncoarray genotypes.

[Nicklas Nordborg]

In 7742:

References #1596: Display genotypes for a single variant in it's own column

Do not display the "Add column" icon for SNPs that are already displayed as columns.

[Nicklas Nordborg]

In 7743:

References #1596: Display genotypes for a single variant in it's own column

Changes to make it easier for subclasses to set their own column properties.

[Nicklas Nordborg]

In 7744:

References #1596: Display genotypes for a single variant in it's own column

Implemented support for the imputed genotypes (no filtering functionality yet).

[Nicklas Nordborg]

In 7757:

References #1596: Display genotypes for a single variant in it's own column

Implemented filtering for imputed SNP columns.

[Nicklas Nordborg]

In 7758:

References #1596: Display genotypes for a single variant in it's own column

Make sure that the VCF parser is closed.

[Nicklas Nordborg]

In 7759:

References #1596: Display genotypes for a single variant in it's own column

Updated to BASE 3.19.12 and use the new export title feature.

[Nicklas Nordborg]

In 7760:

References #1596: Display genotypes for a single variant in it's own column

Implemented support for regular variant calls (RNAseq and WGS). Filtering is not yet implemented.

[Nicklas Nordborg]

In 7761:

References #1596: Display genotypes for a single variant in it's own column

Added filtering support for regular variant calls.

[Nicklas Nordborg]

In 7762:

References #1596: Display genotypes for a single variant in it's own column

Fixes some issues when displaying list of variants in a popup. The "Add column" icon should not be included in this case. Also found some bugs that causes bioassay and file IDs to not be submitted/used correctly.

[Nicklas Nordborg]

In 7763:

References #1596: Display genotypes for a single variant in it's own column

Include the gene name in the column subheader. Some changes to the CSS to make it easier to read.

[Nicklas Nordborg]

In 7764:

References #1596: Display genotypes for a single variant in it's own column

Added a "zoom" icon to the genotypes that opens the same popup with more details about the variant.

[Nicklas Nordborg]

In 7767:

References #1596: Display genotypes for a single variant in it's own column

Implemented support for SNP columns as parent/child columns.