Use DNA genotyping in the Genotype QC wizards

[Nicklas Nordborg]

Now that the genotyping information from the blood DNA samples have been integrated into BASE it would be nice if the genotype information could be used by the Genotype QC wizards.

[Nicklas Nordborg]

In 6588:

References #1361: Use DNA genotyping in the Genotype QC wizards

The genotype calls are now used in the first Genotype QC wizard. Some changes may cause the Flagged alignment wizard to stop working.

[Nicklas Nordborg]

In 6589:

References #1361: Use DNA genotyping in the Genotype QC wizards

The "Flagged alignments" wizard should now be able to use the genotyping information from GenotypeCall items.

[Nicklas Nordborg]

In 6590:

References #1361: Use DNA genotyping in the Genotype QC wizards

Include information about the BeadChip when comparing against genotype calls.

[Nicklas Nordborg]

In 6591:

References #1361: Use DNA genotyping in the Genotype QC wizards

Errors during pre-loading are now catched and displayed for the user instead of the progress bar getting stuck somewhere in the middle.

[Nicklas Nordborg]

In 6592:

References #1361: Use DNA genotyping in the Genotype QC wizards

Display bead chip name instead of barcode.

[Nicklas Nordborg]

In 6594:

References #1361: Use DNA genotyping in the Genotype QC wizards

Create a local copy of VCF files that are located on remote servers. This will improve performance when used in the future.

[Nicklas Nordborg]

In 6595:

References #1361: Use DNA genotyping in the Genotype QC wizards

Updated the standalone genotype check wizard.

[Nicklas Nordborg]

In 6596:

References #1361: Use DNA genotyping in the Genotype QC wizards

Found some stray files that should be removed.

[Nicklas Nordborg]

In 6598:

References #1361: Use DNA genotyping in the Genotype QC wizards

The local copy should not be compressed.