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MethylationAnnotation

holodeck_lib::meth

Struct MethylationAnnotation 

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pub struct MethylationAnnotation {
    pub conversion_type: ConversionType,
    pub conversion_failed: bool,
    pub r1_pre_conversion_bases: Option<Vec<u8>>,
    pub r2_pre_conversion_bases: Option<Vec<u8>>,
    pub r1_call_tags: Option<CallTags>,
    pub r2_call_tags: Option<CallTags>,
}
Expand description

Annotation captured during methylation read generation, used by downstream writers (notably the golden BAM) to emit the full Bismark- compatible methylation tag set: XG:Z (genome-strand indicator), XR:Z (read-conversion direction; derived from the SAM flag at emission time), YS:Z (pre-conversion bases), the holodeck cf:i conversion-failure flag, plus the Bismark call tags XM:Z / YM:Z / NM:i / MD:Z carried in r1_call_tags / r2_call_tags and computed by crate::methylation_tags::populate_pair_call_tags.

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§conversion_type: ConversionType

Conversion direction for the source fragment (same for R1 and R2).

§conversion_failed: bool

Whether the source molecule was drawn as a conversion failure. A molecule property, so it is identical for R1 and R2; surfaced in the golden BAM as the cf:i ground-truth tag.

§r1_pre_conversion_bases: Option<Vec<u8>>

R1 pre-conversion bases. None when capture_pre_conversion was false at simulation time.

§r2_pre_conversion_bases: Option<Vec<u8>>

R2 pre-conversion bases. None for SE reads or when capture_pre_conversion was false.

§r1_call_tags: Option<CallTags>

R1 Bismark-style methylation call tags (XM, YM, NM, MD). Populated by the simulator when the golden BAM is requested.

§r2_call_tags: Option<CallTags>

R2 Bismark-style methylation call tags. None for SE reads or when the golden BAM is not requested.

Implementations§

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impl MethylationAnnotation

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pub fn r1_tags(&self) -> Option<MethylationRecordTags<'_>>

Tags for the R1 BAM record. Returns None when the pre-conversion bases were not captured (e.g., the user requested bisulfite simulation but not a golden BAM).

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pub fn r2_tags(&self) -> Option<MethylationRecordTags<'_>>

Tags for the R2 BAM record. None for SE pairs OR when pre-conversion bases were not captured.

Trait Implementations§

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impl Clone for MethylationAnnotation

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fn clone(&self) -> MethylationAnnotation

Returns a duplicate of the value. Read more
1.0.0 (const: unstable) · Source§

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

Performs copy-assignment from source. Read more
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impl Debug for MethylationAnnotation

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

Formats the value using the given formatter. Read more

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