rework pileup to by default store results in memory.

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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rework pileup to by default store results in memory. #42

Closed kriemo closed 2 years ago

kriemo commented 2 years ago

reduces disk i/o by avoiding writing pileup, indexing with tabix, then reading into R. Also using dev rhtslib 1.99, so no need to copy bedidx from samtools.