Documentation
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Index ¶
- Constants
- func BuildENALookup(dir string, f ENAFilter, keep map[string]struct{}) (map[string]ENARecord, error)
- func BuildENASampleSet(dir string, f ENAFilter) (map[string]struct{}, error)
- func SortResults(rows []ResultRow, sortBy string, desc bool)
- type ENAFilter
- type ENARecord
- type FilterFile
- type Filters
- func (f *Filters) HasRunFilter() bool
- func (f *Filters) HasSampleFilter() bool
- func (f *Filters) LoadRunFile() error
- func (f *Filters) LoadSampleFile() error
- func (f *Filters) MatchesGenus(species string) bool
- func (f *Filters) MatchesSpecies(species string) bool
- func (f *Filters) MatchesSpeciesLike(species string) bool
- func (f *Filters) NeedsAssemblyStats() bool
- func (f *Filters) NeedsCheckM2() bool
- func (f *Filters) NeedsENA() bool
- func (f *Filters) NeedsSylph() bool
- func (f *Filters) RunAccessions() []string
- func (f *Filters) SampleAccessions() []string
- func (f *Filters) SampleSet() map[string]struct{}
- type OutputConfig
- type QueryPlan
- type ResultRow
Constants ¶
const ENAFileName = "ena_20250506.parquet"
ENAFileName is the name of the ENA metadata parquet file on disk.
Variables ¶
This section is empty.
Functions ¶
func BuildENALookup ¶
func BuildENALookup(dir string, f ENAFilter, keep map[string]struct{}) (map[string]ENARecord, error)
BuildENALookup streams ena_20250506.parquet and returns a map of sample_accession -> ENARecord for every row matching the filter.
When keep is non-nil, rows whose sample_accession is not in keep are skipped, so callers that already have a result set only materialise records they will use. First match wins when a sample has multiple ENA rows.
Returns (nil, nil) when the filter is inactive and keep is nil, so callers can skip the scan entirely.
func BuildENASampleSet ¶
BuildENASampleSet is the set-only variant of BuildENALookup. Retained for callers that only need the intersection key set.
func SortResults ¶
SortResults sorts rows in place by the given column. If sortBy is empty, it is a no-op. Numeric values are compared numerically; everything else falls back to lexicographic string comparison.
Types ¶
type ENAFilter ¶
type ENAFilter struct {
Country string
Platform string
CollectionDateFrom string
CollectionDateTo string
}
ENAFilter holds optional filters that require joining against the ENA metadata table. It is the subset of Filters that any command can reuse without pulling in the full query Filters struct.
type ENARecord ¶
ENARecord is the subset of ENA columns exposed in output rows. It is deliberately narrow so that enrichment maps stay small even when the ENA table has millions of entries.
type FilterFile ¶
type FilterFile struct {
Filter Filters `toml:"filter"`
Output OutputConfig `toml:"output"`
}
FilterFile is the top-level structure for a TOML filter file.
func LoadFilterFile ¶
func LoadFilterFile(path string) (*FilterFile, error)
LoadFilterFile parses a TOML filter file at the given path.
type Filters ¶
type Filters struct {
Species string `toml:"species"`
SpeciesLike string `toml:"species_like"`
Genus string `toml:"genus"`
Samples []string `toml:"samples"`
SampleFile string `toml:"sample_file"`
Runs []string `toml:"runs"`
RunFile string `toml:"run_file"`
HQOnly bool `toml:"hq_only"`
MinCompleteness float64 `toml:"min_completeness"`
MaxContamination float64 `toml:"max_contamination"`
MinN50 int64 `toml:"min_n50"`
Dataset string `toml:"dataset"`
HasAssembly bool `toml:"has_assembly"`
Country string `toml:"country"`
Platform string `toml:"platform"`
CollectionDateFrom string `toml:"collection_date_from"`
CollectionDateTo string `toml:"collection_date_to"`
// contains filtered or unexported fields
}
Filters holds all query filter criteria.
func (*Filters) HasRunFilter ¶ added in v0.21.0
HasRunFilter reports whether any run accession filter is active.
func (*Filters) HasSampleFilter ¶
HasSampleFilter reports whether any sample filter is active.
func (*Filters) LoadRunFile ¶ added in v0.21.0
LoadRunFile reads run accessions from the file referenced by RunFile. Lines starting with # and blank lines are skipped.
func (*Filters) LoadSampleFile ¶
LoadSampleFile reads sample accessions from the file referenced by SampleFile. Lines starting with # and blank lines are skipped.
func (*Filters) MatchesGenus ¶ added in v0.22.0
MatchesGenus matches the Genus filter against the genus token of a species name, treating GTDB alphabetic suffixes as equivalent so "Enterococcus" matches "Enterococcus_A faecium". An empty filter matches everything.
func (*Filters) MatchesSpecies ¶
MatchesSpecies matches the Species filter against a species name, treating GTDB alphabetic suffixes as equivalent so an NCBI-style query ("Enterococcus faecium") matches the GTDB-split names stored in the data ("Enterococcus_A faecium"). An empty filter matches everything.
func (*Filters) MatchesSpeciesLike ¶
MatchesSpeciesLike performs a wildcard match using % against the SpeciesLike filter. An empty filter matches everything.
func (*Filters) NeedsAssemblyStats ¶
NeedsAssemblyStats reports whether assembly statistics are required.
func (*Filters) NeedsCheckM2 ¶
NeedsCheckM2 reports whether CheckM2 quality metrics are required.
func (*Filters) NeedsENA ¶
NeedsENA reports whether ENA metadata (country, platform, dates) is required.
func (*Filters) NeedsSylph ¶
NeedsSylph is reserved for future use and always returns false.
func (*Filters) RunAccessions ¶ added in v0.21.0
RunAccessions returns the deduplicated union of the Runs slice and any accessions loaded from a run file, preserving first-seen order.
func (*Filters) SampleAccessions ¶ added in v0.17.1
SampleAccessions returns the deduplicated union of the Samples slice and any accessions loaded from a sample file, preserving first-seen order. It is the slice counterpart to SampleSet, suitable for building SQL IN clauses.
type OutputConfig ¶
type OutputConfig struct {
Columns []string `toml:"columns"`
SortBy string `toml:"sort_by"`
SortDesc bool `toml:"sort_desc"`
Limit int `toml:"limit"`
Offset int `toml:"offset"`
Format string `toml:"format"`
Output string `toml:"output"`
}
OutputConfig controls how query results are formatted and written.
type QueryPlan ¶
type QueryPlan struct {
Tables []string
}
QueryPlan describes which parquet tables to read for a query.
Source Files