Crate salmon_align 

salmon-align: alignment-based (BAM) quantification.

The alternative to mapping FASTQ reads: take a BAM of reads already aligned to the transcriptome (each @SQ is a transcript) and quantify directly from those alignments. References and their lengths come from the BAM header, so no index or FASTA is required for basic quantification.

For each fragment (the contiguous run of records sharing a read name) the set of transcripts it aligns to becomes an equivalence class, weighted by alignment score (AS) via the same exp(-scoreExp·(best−score)) rule used in the mapping path. Fragment lengths (TLEN) feed the fragment-length distribution. The class set then flows through the shared EM (salmon_infer) to quant.sf. Mirrors salmon’s quant -a mode (the position-binned alignment error model is a later refinement).

Structs

AlignQuantOptions

Options for alignment-based quantification.

AlignQuantResult

Quantification results.

Functions

quantify_alignments

Run alignment-based quantification end-to-end.