dot-gmultitasking_strategy: Choose the multitasking strategy for gextract

In misha: Toolkit for Analysis of Genomic Data

Choose the multitasking strategy for gextract

Description

Read getOption("gmultitasking.strategy", "auto") and resolve "auto" to either "tiles" (the historical misha multitask: each kid handles a tile range across all tracks) or "tracks" (R-side mclapply: each worker handles a track subset across all tiles). Track-parallel is a major win on cold-NFS many-track gextract workloads (~5× measured on Tamar's 30-track × 2.19M-bin bench) because each worker only mmap-faults its own files, avoiding the working-set thrashing that 24 kids × 500 tracks creates on the kernel page cache.

Usage

.gmultitasking_strategy(
  tracks,
  intervals,
  iterator = NULL,
  file = NULL,
  intervals.set.out = NULL,
  band = NULL
)

Arguments

tracks	character vector of track expressions
intervals	data.frame of intervals (or NULL for big intervals sets)
file	optional output file path (NULL = data.frame return)
intervals.set.out	optional bigset output name
band	optional 2D band parameter

Details

Falls back to "tiles" when track-parallel doesn't apply (single track, file/bigset output, 2D band iteration, or workload too small to amortize fork overhead).

Value

one of "tiles" or "tracks"

misha documentation built on Aug. 24, 2026, 5:14 p.m.