redst4r / bustools_cli-rs

Bustools CLI implementation in Rust

Readme

Rust version of bustools command line interface. At this point, it's far from complete and correct, but rather a project to learn rust.

This is heavly built on rustbustools, which handles all the basic interactions with busfiles.

Example

# sorting
rustbustools --output /tmp/sorted.bus sort --ifile /tmp/unsorted.bus

# correcting CBs
rustbustools --output /tmp/corrected.bus sort --ifile /tmp/sorted.bus --whitelist /tmp/10x_whitelist.txt

# inspecting
rustbustools --output /dev/null --ifile /tmp/sorted.bus

# count
rustbustools --output /tmp/count_folder --ifile /tmp/sorted.bus --t2g /tmp/transcripts_to_gene.txt

# compression
# -N is the chunksize of a busz block
rustbustools --output /tmp/compressed.busz -i /tmp/sorted.bus -N 10000

# decompression
rustbustools --output /tmp/plain.bus -i /tmp/compressed.busz

Todo 08/05

• performance checks
  • sort: seems to be slow
  • correct: some performance issues due to BKTree
  • count: slightly slower than original bustools, but its in the ballpark
  • inspect: pretty quick already
  • butterfly amplfication: pretty quick already
• handle compressed busfiles
• make CLI args compatible/consistent with original bustools