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Add pair_id property to Rearrangement object

Chain-pairing and single-cell resolution will not always conincide
with each other, as single-cell experiments could only sequence one
locus while stochastic pairing can infer associated chains from
bulk sequencing samples. To reflect this, an additional `pair_id`
key is introduced to the Rearrangement object.
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bussec committed Apr 23, 2019
1 parent 34f34fe commit b378088c985ca44ad7ba9b72800cf5b3a300f999
Showing with 42 additions and 3 deletions.
  1. +14 −1 lang/R/inst/extdata/airr-schema.yaml
  2. +14 −1 lang/python/airr/specs/airr-schema.yaml
  3. +14 −1 specs/airr-schema.yaml
@@ -1785,6 +1785,19 @@ Rearrangement:
set: 6
subset: data (processed sequence)
name: Read count
pair_id:
type: string
description: >
Valid sequence_id that was determined by experimental or computational means to
be associated with the current Rearrangement on the cellular level.
example: ABC314159
x-airr:
miairr: true
required: true
nullable: true
set: 6
subset: data (processed sequence)
name: Paired-chain index
cell_id:
type: string
description: >
@@ -1796,7 +1809,7 @@ Rearrangement:
nullable: true
set: 6
subset: data (processed sequence)
name: Cell Index
name: Cell index
clone_id:
type: string
description: Clonal cluster assignment for the query sequence.
@@ -1785,6 +1785,19 @@ Rearrangement:
set: 6
subset: data (processed sequence)
name: Read count
pair_id:
type: string
description: >
Valid sequence_id that was determined by experimental or computational means to
be associated with the current Rearrangement on the cellular level.
example: ABC314159
x-airr:
miairr: true
required: true
nullable: true
set: 6
subset: data (processed sequence)
name: Paired-chain index
cell_id:
type: string
description: >
@@ -1796,7 +1809,7 @@ Rearrangement:
nullable: true
set: 6
subset: data (processed sequence)
name: Cell Index
name: Cell index
clone_id:
type: string
description: Clonal cluster assignment for the query sequence.
@@ -1785,6 +1785,19 @@ Rearrangement:
set: 6
subset: data (processed sequence)
name: Read count
pair_id:
type: string
description: >
Valid sequence_id that was determined by experimental or computational means to
be associated with the current Rearrangement on the cellular level.
example: ABC314159
x-airr:
miairr: true
required: true
nullable: true
set: 6
subset: data (processed sequence)
name: Paired-chain index
cell_id:
type: string
description: >
@@ -1796,7 +1809,7 @@ Rearrangement:
nullable: true
set: 6
subset: data (processed sequence)
name: Cell Index
name: Cell index
clone_id:
type: string
description: Clonal cluster assignment for the query sequence.

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