Struct DeflateIndex

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pub struct DeflateIndex { /* private fields */ }

Expand description

An in-memory random-access index for a DEFLATE-based stream.

Implementations§

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impl DeflateIndex

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pub fn new() -> Self

Returns an empty index.

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pub const fn kind(&self) -> IndexKind

Returns the source/container provenance recorded by this index.

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pub const fn set_kind(&mut self, kind: IndexKind)

Records source/container provenance.

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pub const fn compressed_size(&self) -> Option<u64>

Returns the known compressed source size in bytes.

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pub const fn set_compressed_size(&mut self, size: Option<u64>)

Records the compressed source size, or clears it when unknown.

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pub const fn uncompressed_size(&self) -> Option<u64>

Returns the known total decompressed size in bytes.

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pub const fn set_uncompressed_size(&mut self, size: Option<u64>)

Records the total decompressed size, or clears it when unknown.

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pub const fn checkpoint_spacing(&self) -> Option<u64>

Returns the target decompressed checkpoint spacing, when recorded.

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pub const fn set_checkpoint_spacing(&mut self, spacing: Option<u64>)

Records the target decompressed checkpoint spacing.

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pub const fn total_line_count(&self) -> Option<u64>

Returns the total line count carried by the source index.

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pub const fn set_total_line_count(&mut self, count: Option<u64>)

Records the total line count, or clears it when unknown.

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pub fn push( &mut self, checkpoint: Checkpoint, window: StoredWindow, ) -> Result<(), IndexError>

Appends a checkpoint and its predecessor window.

Ordering is not checked here; call Self::validate once the index is complete.

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pub fn checkpoint_count(&self) -> usize

Returns the number of checkpoints.

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pub fn is_empty(&self) -> bool

Returns whether the index holds no checkpoints.

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pub fn checkpoints(&self) -> &[Checkpoint]

Returns the checkpoints in order.

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pub const fn windows(&self) -> &WindowMap

Returns the stored predecessor windows.

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pub fn checkpoint_at_or_before( &self, uncompressed_offset: u64, ) -> Option<&Checkpoint>

Returns the last checkpoint at or before uncompressed_offset.

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pub fn checkpoint_at_or_before_line(&self, line: u64) -> Option<&Checkpoint>

Returns the latest checkpoint proven not to be after zero-based line’s start.

A line offset is the number of newline bytes preceding a checkpoint. A checkpoint with the same offset as line may already be inside that line, so targets after line zero resume from the last checkpoint with a strictly smaller line offset. Line zero resumes from a checkpoint at decoded offset zero. This returns None unless the index has a total line count and every checkpoint is annotated, because selecting from partially annotated metadata could skip past the requested line.

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pub fn write_native(&self, writer: &mut impl Write) -> Result<(), IndexError>

Writes this index in the crate’s native versioned format.

The native format is the only one that round-trips every field, including line offsets and compressed window payloads.

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pub fn read_native(reader: &mut impl Read) -> Result<Self, IndexError>

Reads an index written by Self::write_native.

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pub fn read_native_with_options( reader: &mut impl Read, options: IndexReadOptions, ) -> Result<Self, IndexError>

Reads a native index using explicit untrusted-input limits.

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pub fn write_gzidx(&self, writer: &mut impl Write) -> Result<(), IndexError>

Writes this index in indexed_gzip GZIDX version 1 format.

Every non-empty window is written as exactly WINDOW_SIZE bytes.

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pub fn read_gzidx( reader: &mut impl Read, archive_size: Option<u64>, ) -> Result<Self, IndexError>

Reads an indexed_gzip GZIDX index, accepting versions 0 and 1.

When archive_size is Some, it must equal the compressed size stored in the index header.

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pub fn read_gzidx_with_options( reader: &mut impl Read, archive_size: Option<u64>, options: IndexReadOptions, ) -> Result<Self, IndexError>

Reads a GZIDX index using explicit untrusted-input limits.

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pub fn write_gzi(&self, writer: &mut impl Write) -> Result<(), IndexError>

Writes this index in htslib BGZF .gzi format.

Only indexes whose checkpoints all sit on independent member or block boundaries can be represented; a checkpoint carrying a predecessor window or a non-byte-aligned offset is refused, because reimporting it would install an empty window and seek to the wrong place.

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pub fn read_gzi( reader: &mut impl Read, archive_size: Option<u64>, ) -> Result<Self, IndexError>

Reads an htslib BGZF .gzi index.

The format does not record the uncompressed size, so the result leaves it unknown. archive_size, when supplied, is recorded as the compressed size.

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pub fn read_gzi_with_options( reader: &mut impl Read, archive_size: Option<u64>, options: IndexReadOptions, ) -> Result<Self, IndexError>

Reads a .gzi index using explicit untrusted-input limits.

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pub fn write_gztool( &self, writer: &mut impl Write, lines: WithLines, ) -> Result<(), IndexError>

Writes this index in gztool format.

WithLines::Yes writes version 1 with per-point line counters; WithLines::No writes version 0 and omits them. Windows are stored zlib-compressed, as gztool does.

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pub fn read_gztool( reader: &mut impl Read, archive_size: Option<u64>, ) -> Result<Self, IndexError>

Reads a complete gztool index of either version.

gztool does not record the compressed archive size, so archive_size, when supplied, is recorded as the compressed size.

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pub fn read_gztool_with_options( reader: &mut impl Read, archive_size: Option<u64>, options: IndexReadOptions, ) -> Result<Self, IndexError>

Reads a gztool index using explicit untrusted-input limits.

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pub fn validate(&self) -> Result<(), IndexError>

Checks the index invariants.

Compressed offsets must increase strictly and decompressed offsets must not decrease. Every non-empty window must be exactly WINDOW_SIZE bytes, and offsets must fall inside the recorded sizes when those are known.