Module bustools::consistent_genes

This module handles the Equivalance class to gene mapping

An EC represents a set of transcripts which the read is consistent with. This is then mapped to genes:

• the EC resolves to a single gene, clear case for a count
• the EC resolves to multipel genes (the read aligned to a part of the transcriptome which is ambigous)

It gets more complicated if we have multiple ECs for an mRNA, i.e. multiple busrecords with same CB/UMI, but different EC This happens since mRNAs get fragmented after amplification, and different fragments can map to different parts
of the transcriptome, hence yielding different ECs

See Ec2GeneMapper and MappingResult

Structs

• CB
  Thin wrapper around u64, a cell-barcode
• CUGset
  Represents a busrecord (actually an observed CB/UIM combination) with a set of consistent genes (genes that this CB/UMI could map to) and the number of times this combination was seen in the busfile
• EC
  Thin wrapper aroud u32, representing an Equivalence Class
• Ec2GeneMapper
  Deals with the EC (equivalence class) to gene mapping Resolve a given EC into a set of genes consistent with that EC
• GeneId
  Gene identifier
• Genename
  Name of a particular gene

Enums

• InconsistentResolution
  if we come across a CB/UMI the has inconsistent mapping i.e. mapping to 2 different genes, how to handle
• MappingMode
• MappingResult
  MappingResult represents an attempt to unify several BusRecords with matching CB/UMI into an mRNA expressed from a single gene.

Functions

• find_consistent
  For a set of busrecords (coming from the same molecule), this function tries to map those records to genes consistently.
• groubygene
  Group a set of busrecords (same CB/UMI) by genes they are consistent with