Documentation
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Overview ¶
Package runs maps sequencing run accessions (ERR/SRR/DRR) onto the sample accessions the rest of AllTheBacteria is keyed by.
Index ¶
Constants ¶
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Variables ¶
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Functions ¶
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Types ¶
type Resolution ¶
type Resolution struct {
// Samples are the distinct sample accessions the runs belong to, sorted.
Samples []string
// Missing are the requested run accessions the mapping table does not
// list, in the order they were requested.
Missing []string
}
Resolution is the outcome of mapping run accessions onto sample accessions.
func Resolve ¶
func Resolve(path string, runAccessions []string) (Resolution, error)
Resolve maps run accessions to sample accessions using the run.parquet mapping table at path.
A run may name more than one sample. The table records those as a comma-joined list in a single field, so every field is split. Rows are not filtered on the table's pass column: resolving an accession is a lookup, and quality filtering belongs to the query flags.
An empty request returns an empty resolution without opening the file.
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