BedRecord

Mojo struct 🡭

BedRecord

@memory_only
struct BedRecord

Single BED feature (owned). Coordinates are 0-based, half-open.

score: UInt16 in [0, 1000] per BED spec. OtherFields: extra columns beyond the standard BED12 fields (or beyond field 9 for BED10/11), stored as owned strings.

Fields

• Chrom (BString)
• ChromStart (UInt64)
• ChromEnd (UInt64)
• Name (Optional[BString])
• Score (Optional[UInt16])
• Strand (Optional[Strand])
• ThickStart (Optional[UInt64])
• ThickEnd (Optional[UInt64])
• ItemRgb (Optional[ItemRgb])
• BlockSizes (Optional[List[UInt64]])
• BlockStarts (Optional[List[UInt64]])
• OtherFields (Optional[List[BString]])
• NumFields (Int)

Implemented traits

AnyType, Copyable, Deinitable, Movable, Writable

Methods

chrom

fn def chrom(ref self) -> String

Args:

• self (Self)

Returns:

String

start_position

fn def start_position(self) -> Position

1-based start of the feature (aligned with noodles_core; BED chromStart → start+1).

Args:

• self (Self)

Returns:

Position

end_position

fn def end_position(self) -> Optional[Position]

1-based end position (ChromEnd). None for zero-length BED records (ChromEnd == 0).

Args:

• self (Self)

Returns:

Optional[Position]

interval

fn def interval(self) -> Optional[Interval]

Feature extent as 1-based closed [ChromStart+1, ChromEnd]. Returns None for zero-length BED records (ChromEnd == 0). BED 0-based half-open [s, e) → 1-based closed [s+1, e].

Args:

• self (Self)

Returns:

Optional[Interval]

thick_interval

fn def thick_interval(ref self) -> Optional[Interval]

Thick (coding) extent if fields 7–8 present; else None (1-based closed).

Args:

• self (Self)

Returns:

Optional[Interval]

name

fn def name(ref self) -> Optional[String]

Args:

• self (Self)

Returns:

Optional[String]

item_rgb

fn def item_rgb(ref self) -> Optional[ItemRgb]

Args:

• self (Self)

Returns:

Optional[ItemRgb]

block_sizes

fn def block_sizes(ref self) -> Optional[List[UInt64]]

Args:

• self (Self)

Returns:

Optional[List[UInt64]]

block_starts

fn def block_starts(ref self) -> Optional[List[UInt64]]

Args:

• self (Self)

Returns:

Optional[List[UInt64]]

other_fields

fn def other_fields(ref self) -> Optional[List[String]]

Return extra columns beyond the standard BED fields, if any.

Args:

• self (Self)

Returns:

Optional[List[String]]

write_to

fn def write_to[w: Writer](ref self, mut writer: w)

Write this record as one TAB-delimited line (same column count as parsed).

Parameters:

• w (Writer)

Args:

• self (Self)
• writer (w)