More functionality in the Flagged alignment wizard

[Nicklas Nordborg]

See #1046. It is currently a read-only wizard that can be used for investigations. It needs more functionality:

• [Done] We need to add support for scheduling re-extractions, etc.
• [Postponed, #1054] When a problem has been "solved" we need to be able to remove items from the "Flagged alignments" list. Items that are contaminated or a mixup need to be flagged or handled in some way (not yet decided). Items that are ok should be unflagged and be uses as if nothing had happened.
• [Done] Load information about all RNA/Library items even if we have no alignment for them. This can help in problem solving (for example, if we get a low mismatch we can try to find another RNA for the same patient even if we don't have any alignment for that RNA).
• ... and possible more ...

[Nicklas Nordborg]

(In [4817]) References #1050: More functionality in the Flagged alignment wizard

Added functionality for scheduling re-processing. When a filter is active the wizard can now be used in "Schedule re-proccsing" mode which changes the table to display information about the remaining quantity of "Specimen", "Lysate" and "RNA". It is possible to schedule re-processing from either one of them.

[Nicklas Nordborg]

(In [4818]) References #1050: More functionality in the Flagged alignment wizard

When a QiaCube or LibPlate filter is active the wizard will now load information about RNA/Libraries that there is no alignment that we can use for genotyping. This means for example that:

• Low mismatches to an unexpected patient can be traced to another RNA on a QiaCube even if we didn't get enough RNA to sequence on that QiaCube.
• Re-processing can be scheduled for all items.
• External libraries on a LibPlate are listed (but not used in genotyping).

[Nicklas Nordborg]

(In [4819]) References #1050: More functionality in the Flagged alignment wizard

Sort warnings/messages by category and alignment name to avoid re-ordering of messages when switching filters.

[Nicklas Nordborg]

(In [4820]) References #1050: More functionality in the Flagged alignment wizard

Fixed a problem with re-processing RNA (or Library) with no alignment. The selection was based on the ID of the alignment which failed if there was no alignment but only a RNA or Library. The selection is now based on the ordinal number in the list instead.

[Nicklas Nordborg]

(In [4821]) References #1050: More functionality in the Flagged alignment wizard

The wizard now load alignments without a filter on the QC_GENOTYPE_STATUS annotation. Genotyping is only performed if the status is "Checked", but now we can display more information and a message Genotyping is disabled for this alignment (instead of No alignement from this RNA/Library).

[Nicklas Nordborg]

(In [4823]) References #1050: More functionality in the Flagged alignment wizard

Changes the order and conditions for generating messages about an alignment. This should avoid some seemingly contradicting messages (for example: 'No alignment from this RNA' and 'Genotyping is disabled for this alignment').