Implement a new Genotype QC wizard for validating WGS data

[Nicklas Nordborg]

This is related to #1483. But before the WGS data can be used in the existing wizards we need to be able to verify the WGS genotypes against the RNAseq data.

As long as the genotypes (from blood) matches we should be good to go and mark the RNAseq as "Verified by DNA". Exactly how to handle mismatches has not been decided yet.

[Nicklas Nordborg]

In 7211:

References #1487: Implement a new Genotype QC wizard for validating WGS data

Added a new wizard for the normal WGS alignments. It can compare with existing items, but registration is probably not doing the correct thing. The possible and default actions need to be a bit different than for the RNAseq wizard.

[Nicklas Nordborg]

In 7212:

References #1483 and #1487.

Implemented support for multi-threading in the comparison phase. This makes it possible to compare several hundred alignments in one go with reasonable speed.

[Nicklas Nordborg]

In 7213:

References #1487: Implement a new Genotype QC wizard for validating WGS data

Change ordering of results so that items with HIGH warning level are displayed before items with LOW warning level, and then items with messages before items with no messages.

[Nicklas Nordborg]

In 7215:

References #1487: Implement a new Genotype QC wizard for validating WGS data

Implemented registration of the results.

[Nicklas Nordborg]

In 7216:

References #1487: Implement a new Genotype QC wizard for validating WGS data

Automatically set the DoNotUse annotation for alignments with high HET. The annotation is also set for upstream items up to Library.

[Nicklas Nordborg]

In 7217:

References #1487: Implement a new Genotype QC wizard for validating WGS data

Added support for using the QC wizard with Tumor/DNA data. In this case, comparisons with RNAseq data is skipped. The recommended actions are not correct. It should not be possible to flag items since this is only done with RNAseq alignments.

[Nicklas Nordborg]

In 7218:

References #1487: Implement a new Genotype QC wizard for validating WGS data

Recommended actions should now be correct for WGS/Tumor and registration should work.

[Nicklas Nordborg]

In 7219:

References #1487: Implement a new Genotype QC wizard for validating WGS data

It is better if the QC-wizards can check all DNA items in one go, so the limit of 250 is removed for the DNA pipeline.

[Nicklas Nordborg]

In 7220:

References #1487: Implement a new Genotype QC wizard for validating WGS data

Fixes an incorrect "disable" recommendation for High/Low mismatches when used with the DNA/Normal samples.