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Add list of known attributes that can be included in the digest #12

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Add list of known attributes that can be included in the digest #12

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75337c9
Add list of known attributes that can be included in the digest
tcezard Jun 16, 2021
1458f3b
Remove statement about the mandatory field
tcezard Aug 12, 2021
acd6404
Remove order of the list of attributes supported.
tcezard Sep 22, 2021
cb7017a
Update date
tcezard Sep 22, 2021
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19 changes: 19 additions & 0 deletions docs/decision_record.md
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Expand Up @@ -17,3 +17,22 @@ Should a wider GA4GH standard appear from [TASC issue 5](https://github.com/ga4g
### Known limitations

- There have been a handful of reports of old sequences with disallowed characters in the sequence name rows (`>`) of FASTA files, particularly from the microbiome community. These sequence collections would have to be changed to include only SAM-compatible ASCII characters, which could restrict usage of the sequence collections protocols and delay uptake.

## 2021-09-22 - Controlled vocabulary for the supported fields

### Decision

The attributes allowed to be used in the sequence collection digest construction are:
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I'm not sure if 'allowed' is the right word here -- since we allow everything, really. I think it's more like, these are the controlled vocabulary terms for the basic, universal seqcol spec....

Maybe:

"The initial set of controlled vocabulary terms for sequence collection attributes included in the digest construction are: "

And then I think I'd also add to this ADR the decision that additional custom attributes are allowed.

- lengths: the length of the sequences
- sequences: the Refget digests of the sequences
- names: the given name of the sequence in this collection
- topologies: the topology of each sequence (can be either linear or circular)
- priorities: importance of the sequence in the assembly

### Linked issues

- https://github.com/ga4gh/seqcol-spec/issues/8

### Known limitations

- After long discussion, we decided that storing an order array to explicitely was going to bring too many complications so we decided against it. This will limit (but not negate) our ability to find collections that have the same content but where the element. are in a different.
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I think I would just leave this for the other ADR entry that discusses it in detail.