Struct ReadInfo 

pub struct ReadInfo {
    pub ref_index1: i32,
    pub start1: i32,
    pub strand1: u8,
    pub ref_index2: i32,
    pub start2: i32,
    pub strand2: u8,
    pub library: Arc<str>,
    pub cell_barcode: Option<String>,
}

Information about read positions needed for grouping and ordering.

This structure stores genomic position information for one or two reads (paired-end), along with library and optional cell barcode information. The R1/R2 positions are stored in their original order without normalization, matching fgbio’s behavior.

Fields

• ref_index1 - Reference sequence index for R1 (first read of pair)
• start1 - Unclipped 5’ start position for R1
• strand1 - Strand for R1 (0=forward, 1=reverse)
• ref_index2 - Reference sequence index for R2 (or UNKNOWN_REF if unpaired)
• start2 - Unclipped 5’ start position for R2
• strand2 - Strand for R2
• library - Library identifier from RG tag
• cell_barcode - Optional cell barcode for single-cell applications

Ordering

ReadInfo implements Ord matching fgbio’s case class field order:

1. Reference index 1 (R1)
2. Start position 1 (R1)
3. Strand 1 (R1)
4. Reference index 2 (R2)
5. Start position 2 (R2)
6. Strand 2 (R2)
7. Library
8. Cell barcode (optional)

Fields

ref_index1: i32

Reference sequence index for first read

start1: i32

Unclipped 5’ position for first read

strand1: u8

Strand for first read (0=forward, 1=reverse)

ref_index2: i32

Reference sequence index for second read

start2: i32

Unclipped 5’ position for second read

strand2: u8

Strand for second read (0=forward, 1=reverse)

library: Arc<str>

Library identifier (from RG tag). Uses Arc<str> to avoid cloning for every read.

cell_barcode: Option<String>

Optional cell barcode (for single-cell data)

Implementations

impl ReadInfo

pub fn new( ref_index1: i32, start1: i32, strand1: u8, ref_index2: i32, start2: i32, strand2: u8, library: Arc<str>, cell_barcode: Option<String>, ) -> Self

Creates a new ReadInfo, automatically ordering by lower coordinate first.

This constructor automatically normalizes the order so that the read with the genomically earlier position becomes position 1. This matches fgbio’s behavior where the lower of the two mates’ positions comes first.

Arguments

• ref_index1 - Reference index for first read
• start1 - Start position for first read
• strand1 - Strand for first read (0=forward, 1=reverse)
• ref_index2 - Reference index for second read
• start2 - Start position for second read
• strand2 - Strand for second read
• library - Library identifier
• cell_barcode - Optional cell barcode

Returns

A new ReadInfo with reads ordered by genomic position (lower position first)

pub fn single( ref_index: i32, start: i32, strand: u8, library: Arc<str>, cell_barcode: Option<String>, ) -> Self

Creates ReadInfo for a single-end or fragment read.

This constructor is used for unpaired reads or when only one read of a pair is available. The second read fields are set to UNKNOWN values.

Arguments

• ref_index - Reference sequence index
• start - Unclipped 5’ start position
• strand - Strand (0=forward, 1=reverse)
• library - Library identifier
• cell_barcode - Optional cell barcode

Returns

A new ReadInfo for a single read

pub fn unmapped(library: Arc<str>, cell_barcode: Option<String>) -> Self

Creates ReadInfo for an unmapped read.

All position and reference fields are set to UNKNOWN values since the read has no genomic alignment.

Arguments

• library - Library identifier
• cell_barcode - Optional cell barcode

Returns

A new ReadInfo for an unmapped read

pub fn strand_to_byte(positive: bool) -> u8

Converts a strand boolean to a byte representation.

Converts the strand direction to the byte format used by ReadInfo:

• true (positive/forward strand) -> 0
• false (negative/reverse strand) -> 1

Arguments

• positive - true for forward strand, false for reverse

Returns

Byte representation (0 or 1)

pub fn from( template: &Template, cell_tag: Tag, library_lookup: &LibraryLookup, ) -> Result<Self>

Builds a ReadInfo from a template.

Extracts position information from the template’s reads, including unclipped 5’ positions, library information from the header’s @RG line (via library lookup), and optional cell barcode.

Arguments

• template - The template containing one or two reads
• cell_tag - SAM tag to use for extracting cell barcode (e.g., “CB”)
• library_lookup - Lookup table mapping read group IDs to library names

Returns

A new ReadInfo populated from the template

Errors

Returns an error if:

• The template has no records
• The unclipped position could not be computed (e.g., missing alignment data)

Trait Implementations

impl Clone for ReadInfo

fn clone(&self) -> ReadInfo

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for ReadInfo

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Hash for ReadInfo

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl Ord for ReadInfo

fn cmp(&self, other: &Self) -> Ordering

Compares ReadInfo in the same order as fgbio’s case class field order: refIndex1, start1, strand1, refIndex2, start2, strand2, library, cellBarcode

fn max(self, other: Self) -> Self

where Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Self

where Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

where Self: Sized,

Restrict a value to a certain interval.

impl PartialEq for ReadInfo

fn eq(&self, other: &ReadInfo) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PartialOrd for ReadInfo

fn partial_cmp(&self, other: &Self) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Rhs) -> bool

Tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

Tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Rhs) -> bool

Tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

Tests greater than or equal to (for self and other) and is used by the >= operator.

impl Eq for ReadInfo

impl StructuralPartialEq for ReadInfo