class

Fqix::Index

Inherits Reference < Object

Constants

DEFAULT_CHECKPOINT_SPAN = (4_u64 * 1024_u64) * 1024_u64

DEFAULT_HASH_ALGORITHM = HashAlgorithm::Fnv1a64

DEFAULT_HASH_SEED = 0_u64

DEFAULT_MODE = IndexMode::Sparse

DEFAULT_NAME_INTERVAL = 1024_u32

DEFAULT_NAME_MODE = NameMode::FirstToken

DEFAULT_ORDER_MODE = OrderMode::Lexicographic

MAGIC = IndexFormat::MAGIC_V2

VERSION = IndexFormat::EXACT_VERSION

Constructors

build(gz_path : String, checkpoint_span : UInt64 = DEFAULT_CHECKPOINT_SPAN, mode : IndexMode = DEFAULT_MODE, name_interval : UInt32 = DEFAULT_NAME_INTERVAL, order_mode : OrderMode | Nil = nil) : Index

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build_exact(gz_path : String, checkpoint_span : UInt64 = DEFAULT_CHECKPOINT_SPAN) : Index

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build_sparse(gz_path : String, checkpoint_span : UInt64 = DEFAULT_CHECKPOINT_SPAN, name_interval : UInt32 = DEFAULT_NAME_INTERVAL, order_mode : OrderMode | Nil = nil) : Index

order_mode is the requested sparse read-name order; nil means auto — try each SparseNameTableBuilder::ORDER_CANDIDATES in precedence and persist the first one the FASTQ is monotonic under.

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new(source_path : String, source_size : UInt64, source_mtime : Int64, checkpoint_span : UInt64, mode : IndexMode, name_interval : UInt32, order_mode : OrderMode, fingerprint_algorithm : HashAlgorithm, fingerprint_seed : UInt64, name_mode : NameMode, record_count : UInt64, input_names_sorted : Bool, checkpoint_metas : Array(CheckpointMeta), names : Array(NameEntry), entries : Array(Entry), window_store : WindowStore, format_version : FormatVersion = VERSION, mphf : Mphf | Nil = nil, slots : Array(ExactSlot) = [] of ExactSlot, overflows : Array(ExactOverflowEntry) = [] of ExactOverflowEntry)

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new(source_path : String, source_size : UInt64, source_mtime : Int64, checkpoint_span : UInt64, fingerprint_algorithm : HashAlgorithm, fingerprint_seed : UInt64, name_mode : NameMode, record_count : UInt64, input_names_sorted : Bool, checkpoint_metas : Array(CheckpointMeta), entries : Array(Entry), window_store : WindowStore, format_version : FormatVersion = VERSION, mphf : Mphf | Nil = nil, slots : Array(ExactSlot) = [] of ExactSlot, overflows : Array(ExactOverflowEntry) = [] of ExactOverflowEntry)

Convenience constructor for tests and callers that directly build an exact v2.1 index object.

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read(path : String) : Index

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Class methods

build_entries(records : Array(RawEntry)) : Array(Entry)

v2.1 entry layout. Retained for reader-compatibility specs; this is not the production exact write path (build_exact uses build_mphf_tables).

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build_mphf_tables(records : Array(RawEntry), fingerprint_seed : UInt64) : Tuple(Mphf, Array(ExactSlot), Array(ExactOverflowEntry))

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build_name_table(checkpoints : Array(CheckpointMeta), anchors : Array(SparseNameTableBuilder::Anchor)) : Array(NameEntry)

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checkpoint_for(checkpoints : Array(CheckpointMeta), out_offset : UInt64) : Int32

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default_path(gz_path : String) : String

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guard(name : String, seed : UInt64) : UInt8

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lower_bound(size : Int32, &before_target : Int32 -> Bool) : Int32

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order_mode_label(mode : OrderMode) : String

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Instance methods

checkpoint(id : Int) : Zran::Checkpoint

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checkpoint_metas

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checkpoint_span

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checkpoint_span=(checkpoint_span : UInt64)

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checkpoint_window(id : Int) : Bytes

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entries

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exact?

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find_entries(query : String) : Array(Entry)

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find_exact_candidates(query : String) : Array(ExactCandidate)

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find_floor_name(query : String, normalized : Bool = false) : NameEntry | Nil

Returns the anchor to start scanning from for query: the last anchor ordering strictly before query. The first FASTQ record is always an anchor, so index 0 is a safe lower bound.

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fingerprint_algorithm

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fingerprint_algorithm=(fingerprint_algorithm : HashAlgorithm)

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fingerprint_seed

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fingerprint_seed=(fingerprint_seed : UInt64)

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format_version

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input_names_sorted=(input_names_sorted : Bool)