#1050 closed enhancement (fixed)
More functionality in the Flagged alignment wizard
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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Priority: | major | Milestone: | Reggie v4.18 |
Component: | net.sf.basedb.reggie | Keywords: | |
Cc: |
Description (last modified by )
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 ...
Change History (10)
comment:1 by , 6 years ago
Status: | new → assigned |
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comment:2 by , 6 years ago
comment:3 by , 6 years ago
(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).
comment:4 by , 6 years ago
Description: | modified (diff) |
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comment:5 by , 6 years ago
comment:6 by , 6 years ago
(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.
comment:7 by , 6 years ago
(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
).
comment:8 by , 6 years ago
(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').
comment:9 by , 6 years ago
Description: | modified (diff) |
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Resolution: | → fixed |
Status: | assigned → closed |
comment:10 by , 6 years ago
Description: | modified (diff) |
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(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.