variant filters and making RangedSummarizedExperiment default return from get_pileup - Githubissues

rnabioco / raer

Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments

https://rnabioco.github.io/raer/

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variant filters and making RangedSummarizedExperiment default return from get_pileup #70

Closed kriemo closed 1 year ago

kriemo commented 1 year ago

rename get_pileup to pileup_sites
rework internals to calculate and store per-site statistics from bcftools related to variant positioning within read.
pileup_sites now returns a RangedSummarizedExperiment with the rowData populated with per-site stats/data
updated tests, examples, and vignettes to work with RangedSummarizedExperiment
added option for fractional trimming
fixed bug related to counting query ends in presence of soft-clipping

This PR will change a few user facing options:

the default return from pileup_sites to be a RangedSummarizedExperiment, merge_pileups is no longer needed as a user facing function. a follow up PR will clean up unused code.
FilterParam gains a ftrim_5p and ftrim_3p parameter