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Documentation Index

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An Alignment is an analysis providing sensitive local alignment of a WGS samples against a specific reference genome sample. It has the same properties as an analyses, but lacks the analysis_type field and also includes a tax_id field indicating the taxonmic ID of the genome against which the alignment was performed. At this time, there are no v1 API routes for accessing the alignment statistics (e.g., percent identity, coverage, and depth), but alignments can be viewed on the One Codex platform directly. Here’s an example public alignment and a list of all alignments for that sample:
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$uri
string
Pattern: ^/api/v1/alignments\/[^/]+$
Example:

"/api/v1/alignments/a1b2c3d4e5f67890"

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complete
boolean
default:false
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created_at
string<date-time>

Timestamp for when the object was created on the One Codex platform, encoded as a RFC 3339 timestamp.

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error_msg
string | null
Maximum string length: 255
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job
object

A reference to the versioned job underlying the analysis, e.g., {"$ref": "/api/v1/jobs/d512cb556241440f"}.

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job_args
object

The arguments passed into this analysis (can be null).

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sample
object

A reference to the sample underlying the analysis, e.g., {"$ref": "/api/v1/sample/0ee172af60e84f61"}.

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success
boolean
default:false