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Clone updates #586

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merged 16 commits into from
Apr 25, 2022
Merged

Clone updates #586

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bcorrie Feb 12, 2022
c4b6e8a
Update `_count` field language and add `umi_count` to Rearrangement.
javh Feb 21, 2022
7b53fa7
Merge branch 'master' into clone-update
javh Feb 21, 2022
88facd7
change description back to original
schristley Feb 22, 2022
a9d7c1b
update description
schristley Feb 22, 2022
dd606fc
update description
schristley Feb 22, 2022
6186094
Merge branch 'master' into clone-update
bcorrie Apr 22, 2022
67ff6df
Sync schemas
bcorrie Apr 22, 2022
33f9e01
Merge branch 'clone-update' of https://github.com/airr-community/airr…
bcorrie Apr 22, 2022
5616524
Sync spec
bcorrie Apr 22, 2022
595adf5
Sync with AIRR v2 spec
bcorrie Apr 22, 2022
667d6ef
Update to be synced with v2 spec
bcorrie Apr 22, 2022
481de11
Update nullable attribute
bcorrie Apr 22, 2022
6579a86
Removed spaces
bcorrie Apr 22, 2022
cf6fad5
Adding nullable
bcorrie Apr 22, 2022
a750ac1
More nullable...
bcorrie Apr 22, 2022
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25 changes: 18 additions & 7 deletions lang/R/inst/extdata/airr-schema.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -3557,15 +3557,14 @@ Rearrangement:
consensus_count:
type: integer
description: >
Number of reads contributing to the (UMI) consensus for this sequence.
Number of reads contributing to the UMI consensus or contig assembly for this sequence.
For example, the sum of the number of reads for all UMIs that contribute to
the query sequence.
duplicate_count:
type: integer
description: >
Copy number or number of duplicate observations for the query sequence.
For example, the number of UMIs sharing an identical sequence or the number
of identical observations of this sequence absent UMIs.
For example, the number of identical reads observed for this sequence.
title: Read count
example: 123
x-airr:
Expand All @@ -3574,6 +3573,12 @@ Rearrangement:
set: 6
subset: data (processed sequence)
name: Read count
umi_count:
type: integer
description: >
Number of distinct UMIs represented by this sequence.
For example, the total number of UMIs that contribute to
the contig assembly for the query sequence.
cell_id:
type: string
description: >
Expand Down Expand Up @@ -3760,12 +3765,18 @@ Clone:
junction_end:
type: integer
description: Junction region end position in the alignment (1-based closed interval).
sequence_count:
umi_count:
type: integer
description: Number of Rearrangement records (sequences) included in this clone.
clone_abundance:
description: >
Number of distinct UMIs observed across all sequences (Rearrangement records) in this clone.
clone_count:
type: integer
description: Non-normalized absolute count of the number of members (immune cells) in this clone.
description: >
Absolute count of the size (number of members) of this clone in the repertoire.
This could simply be the number of sequences (Rearrangement records) observed in this clone,
the number of distinct cell barcodes (unique cell_id values),
or a more sophisticated calculation appropriate to the experimental protocol.
Absolute count is provided versus a frequency so that downstream analysis tools can perform their own normalization.
seed_id:
type: string
description: sequence_id of the seed sequence. Empty string (or null) if there is no seed sequence.
Expand Down
25 changes: 18 additions & 7 deletions lang/python/airr/specs/airr-schema.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -3557,15 +3557,14 @@ Rearrangement:
consensus_count:
type: integer
description: >
Number of reads contributing to the (UMI) consensus for this sequence.
Number of reads contributing to the UMI consensus or contig assembly for this sequence.
For example, the sum of the number of reads for all UMIs that contribute to
the query sequence.
duplicate_count:
type: integer
description: >
Copy number or number of duplicate observations for the query sequence.
For example, the number of UMIs sharing an identical sequence or the number
of identical observations of this sequence absent UMIs.
For example, the number of identical reads observed for this sequence.
title: Read count
example: 123
x-airr:
Expand All @@ -3574,6 +3573,12 @@ Rearrangement:
set: 6
subset: data (processed sequence)
name: Read count
umi_count:
type: integer
description: >
Number of distinct UMIs represented by this sequence.
For example, the total number of UMIs that contribute to
the contig assembly for the query sequence.
cell_id:
type: string
description: >
Expand Down Expand Up @@ -3760,12 +3765,18 @@ Clone:
junction_end:
type: integer
description: Junction region end position in the alignment (1-based closed interval).
sequence_count:
umi_count:
type: integer
description: Number of Rearrangement records (sequences) included in this clone.
clone_abundance:
description: >
Number of distinct UMIs observed across all sequences (Rearrangement records) in this clone.
clone_count:
type: integer
description: Non-normalized absolute count of the number of members (immune cells) in this clone.
description: >
Absolute count of the size (number of members) of this clone in the repertoire.
This could simply be the number of sequences (Rearrangement records) observed in this clone,
the number of distinct cell barcodes (unique cell_id values),
or a more sophisticated calculation appropriate to the experimental protocol.
Absolute count is provided versus a frequency so that downstream analysis tools can perform their own normalization.
seed_id:
type: string
description: sequence_id of the seed sequence. Empty string (or null) if there is no seed sequence.
Expand Down
26 changes: 19 additions & 7 deletions specs/airr-schema-openapi3.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -3736,23 +3736,29 @@ Rearrangement:
type: integer
nullable: true
description: >
Number of reads contributing to the (UMI) consensus for this sequence.
Number of reads contributing to the UMI consensus or contig assembly for this sequence.
For example, the sum of the number of reads for all UMIs that contribute to
the query sequence.
duplicate_count:
type: integer
nullable: true
description: >
Copy number or number of duplicate observations for the query sequence.
For example, the number of UMIs sharing an identical sequence or the number
of identical observations of this sequence absent UMIs.
For example, the number of identical reads observed for this sequence.
title: Read count
example: 123
x-airr:
miairr: important
set: 6
subset: data (processed sequence)
name: Read count
umi_count:
type: integer
nullable: true
description: >
Number of distinct UMIs represented by this sequence.
For example, the total number of UMIs that contribute to
the contig assembly for the query sequence.
cell_id:
type: string
nullable: true
Expand Down Expand Up @@ -3962,14 +3968,20 @@ Clone:
type: integer
nullable: true
description: Junction region end position in the alignment (1-based closed interval).
sequence_count:
umi_count:
type: integer
nullable: true
description: Number of Rearrangement records (sequences) included in this clone.
clone_abundance:
description: >
Number of distinct UMIs observed across all sequences (Rearrangement records) in this clone.
clone_count:
type: integer
nullable: true
description: Non-normalized absolute count of the number of members (immune cells) in this clone.
description: >
Absolute count of the size (number of members) of this clone in the repertoire.
This could simply be the number of sequences (Rearrangement records) observed in this clone,
the number of distinct cell barcodes (unique cell_id values),
or a more sophisticated calculation appropriate to the experimental protocol.
Absolute count is provided versus a frequency so that downstream analysis tools can perform their own normalization.
seed_id:
type: string
nullable: true
Expand Down
25 changes: 18 additions & 7 deletions specs/airr-schema.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3557,15 +3557,14 @@ Rearrangement:
consensus_count:
type: integer
description: >
Number of reads contributing to the (UMI) consensus for this sequence.
Number of reads contributing to the UMI consensus or contig assembly for this sequence.
For example, the sum of the number of reads for all UMIs that contribute to
the query sequence.
duplicate_count:
type: integer
description: >
Copy number or number of duplicate observations for the query sequence.
For example, the number of UMIs sharing an identical sequence or the number
of identical observations of this sequence absent UMIs.
For example, the number of identical reads observed for this sequence.
title: Read count
example: 123
x-airr:
Expand All @@ -3574,6 +3573,12 @@ Rearrangement:
set: 6
subset: data (processed sequence)
name: Read count
umi_count:
type: integer
description: >
Number of distinct UMIs represented by this sequence.
For example, the total number of UMIs that contribute to
the contig assembly for the query sequence.
cell_id:
type: string
description: >
Expand Down Expand Up @@ -3760,12 +3765,18 @@ Clone:
junction_end:
type: integer
description: Junction region end position in the alignment (1-based closed interval).
sequence_count:
umi_count:
type: integer
description: Number of Rearrangement records (sequences) included in this clone.
clone_abundance:
description: >
Number of distinct UMIs observed across all sequences (Rearrangement records) in this clone.
clone_count:
type: integer
description: Non-normalized absolute count of the number of members (immune cells) in this clone.
description: >
Absolute count of the size (number of members) of this clone in the repertoire.
This could simply be the number of sequences (Rearrangement records) observed in this clone,
the number of distinct cell barcodes (unique cell_id values),
or a more sophisticated calculation appropriate to the experimental protocol.
Absolute count is provided versus a frequency so that downstream analysis tools can perform their own normalization.
seed_id:
type: string
description: sequence_id of the seed sequence. Empty string (or null) if there is no seed sequence.
Expand Down