Module pack 

Base/quality packing and trusted four-line FASTQ pack paths.

The high-level FASTQ readers expose borrowed records. This module provides the lower-level side-channel representation used when downstream code wants packed two-bit bases, ambiguity masks, and Phred+33 summaries without allocating an owned record per read. Base and quality packing utilities.

Bases are packed four per byte using A=0, C=1, G=2, and T=3. Ambiguous or non-canonical bases are represented by zero bits in the packed byte stream and a set bit in the separate ambiguity mask. Quality helpers interpret input as Phred+33 FASTQ qualities.

Structs

BaseSummary

Summary of a packed DNA sequence.

PackedRecordSummary

Combined base and quality summary for one FASTQ record.

PackedSequence

Packed sequence bytes plus one bit per ambiguous/non-ACGT base.

QualitySummary

Phred+33 quality summary.

TrustedPackSlab

Progress notification for one trusted pack slab.

TrustedPackedPair

Borrowed view of one trusted packed R1/R2 pair.

TrustedPackedRecord

Borrowed view of one trusted packed FASTQ record.

Enums

PackBuffer

Output buffer involved in a packing error.

PackError

Error returned by base or quality packing helpers.

PackKernel

Selected implementation family for base packing.

PackedBase

Decoded base value from a packed sequence.

Traits

TrustedPackSink

Callback interface for trusted streaming pack paths.

Functions

bin_qualities_into

Bin Phred+33 qualities into threshold indexes.

bin_qualities_into_slice

Bin Phred+33 qualities into a caller-provided output slice.

bit_mask_len

Return the number of bytes needed for a one-bit-per-item mask.

is_masked

Return whether index is marked ambiguous in an ambiguity mask.

pack_bases

Pack a sequence into newly allocated packed-base and ambiguity buffers.

pack_bases_and_summarize_qualities_into

Pack bases and summarize Phred+33 qualities into reusable buffers.

pack_bases_into

Pack a sequence into reusable Vec buffers and return base counts.

pack_bases_into_slices

Pack a sequence into caller-provided fixed-size slices.

pack_trusted_fastq

Pack all complete records from an in-memory trusted four-line FASTQ buffer.

pack_trusted_fastq_direct

Pack an in-memory trusted FASTQ buffer with the direct scanner.

pack_trusted_fastq_direct_sink

Pack an in-memory trusted FASTQ buffer with the direct scanner into a sink.

pack_trusted_fastq_read

Stream trusted four-line FASTQ from a reader and invoke a callback per record.

pack_trusted_fastq_read_direct

Stream trusted FASTQ from a reader using the direct scanner.

pack_trusted_fastq_read_direct_sink

Stream trusted FASTQ from a reader using the direct scanner into a sink.

pack_trusted_fastq_read_sink

Stream trusted four-line FASTQ from a reader into a sink.

pack_trusted_fastq_sink

Pack all complete records from an in-memory trusted FASTQ buffer into a sink.

pack_trusted_paired_fastq_read

Stream ordered R1/R2 FASTQ inputs and emit trusted packed pairs.

packed_base_at

Decode one base at index from packed-base and ambiguity buffers.

packed_base_len

Return the number of bytes needed to store base_count two-bit bases.

selected_pack_kernel

Return the base-packing kernel selected for this build and host.

summarize_qualities

Summarize a slice of Phred+33 quality bytes.