CollectionV3

ragc_common::collection

Struct CollectionV3 

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pub struct CollectionV3 { /* private fields */ }
Expand description

Collection V3 - manages metadata for AGC archives

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impl CollectionV3

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pub fn new() -> Self

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pub fn set_config( &mut self, segment_size: u32, kmer_length: u32, batch_size: Option<usize>, )

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pub fn prepare_for_compression(&mut self, archive: &mut Archive) -> Result<()>

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pub fn prepare_for_decompression(&mut self, archive: &Archive) -> Result<()>

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pub fn register_sample_contig( &mut self, sample_name: &str, contig_name: &str, ) -> Result<bool>

Register a sample and contig (idempotent - adds contig to existing sample if needed)

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pub fn add_segment_placed( &mut self, sample_name: &str, contig_name: &str, place: usize, group_id: u32, in_group_id: u32, is_rev_comp: bool, raw_length: u32, ) -> Result<()>

Add segment placement information

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pub fn get_samples_list(&self, sorted: bool) -> Vec<String>

Get list of samples

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pub fn get_no_samples(&self) -> usize

Get number of samples

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pub fn get_no_contigs(&self, sample_name: &str) -> Option<usize>

Get number of contigs in a sample

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pub fn get_no_contig_batches(&self, archive: &Archive) -> Result<usize>

Get number of contig batches from archive

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pub fn get_contig_list(&self, sample_name: &str) -> Option<Vec<String>>

Get contig list for a sample

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pub fn get_sample_desc( &self, sample_name: &str, ) -> Option<Vec<(String, Vec<SegmentDesc>)>>

Get sample descriptor with all contigs and segments

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pub fn get_contig_desc( &self, sample_name: &str, contig_name: &str, ) -> Option<Vec<SegmentDesc>>

Get contig descriptor for a specific contig in a sample

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pub fn get_params(&self) -> (u32, u32)

Get configuration parameters (segment_size, kmer_length)

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pub fn store_batch_sample_names(&mut self, archive: &mut Archive) -> Result<()>

Store sample names batch (with ZSTD compression)

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pub fn load_batch_sample_names(&mut self, archive: &mut Archive) -> Result<()>

Load sample names batch (with ZSTD decompression)

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pub fn load_contig_batch( &mut self, archive: &mut Archive, id_batch: usize, ) -> Result<()>

Load a batch of contigs (names + details)

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pub fn store_contig_batch( &mut self, archive: &mut Archive, id_from: usize, id_to: usize, ) -> Result<()>

Store a batch of contigs (names + details)

Trait Implementations§

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impl Default for CollectionV3

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fn default() -> Self

Returns the “default value” for a type. Read more

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where T: 'static + ?Sized,

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type Error = <U as TryFrom<T>>::Error

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