compression

Code to run benchmarks on BPCells compressed file formats

• compression/bitwidth-stats:
  • Calculate compression statistics for BPCells bitpacked file formats
  • Requires: datasets/atac-process, datasets/rna-process
  • Produces:
    • {RESULTS_ROOT}/raw/compression/bitwidth-stats: Raw (per-sample or per-matrix) statistics files
    • {RESULTS_ROOT}/data_tables/bitwidth-stats
  • Figures: Fig S2
  • Task summary: 49/49 completed. Total time: 3:44:24
• compression/fragments-read-write:
  • Read and write (import) benchmarks for ATAC-seq fragment files
  • Requires: datasets/atac-process
  • Produces:
    • {RESULTS_ROOT}/raw/compression/fragments-read-write: Raw timing outputs
    • {RESULTS_ROOT}/data_tables/compression/fragments-read-write/
  • Figures: Fig 2g-i
  • Task summary: 430/430 completed. Total time: 11 days, 18:17:37
• compression/in-memory-compression
  • Benchmark in-memory compression performance with general-purpose compression algorithms
  • Requires: datasets/atac-process, datasets/rna-process
  • Produces:
    • {RESULTS_ROOT}/raw/compression/in-memory-compression: Raw timing outputs
    • {RESULTS_ROOT}/data_tables/compression/in-memory-compression.tsv.gz
  • Figures: Fig 2e+j, Fig S3a
  • Task summary: 225/225 completed. Total time: 3 days, 10:38:12
• compression/rna-1M-cell
  • Requires: datasets/rna-download
  • Produces:
    • {RESULTS_ROOT}/raw/compression/rna-1M-cell: Raw timing outputs
    • {RESULTS_ROOT}/data_tables/compression/rna-1M-cell.tsv
  • Figures: Fig 2b-d
  • Task summary: 5/5 completed. Total time: 1:09:13