1. James Taylor
  2. bx-python
Issue #39 new

Slow behaviour of BigWigFile.summarize() at low resolution (few kb)

mimakaev
created an issue

BigWigFile.summarize behavior can be extremely slow for long chromosomes at high resolution. The effect is dataset dependent. Sometimes BigWigFile.summarize("chr1",0,250000000,250000) takes 4 seconds, sometimes gets stuck forever. Some datasets work at 1kb. Some datasets get stuck at 1kb, but work fine at 5kb. Other datasets get stuck even at 20kb.

An example is wgEncodeUwDnaseGm06990RawRep1.bigWig that gets stuck at 20 kb.

summarize("chr1",0,240000000,1000) - less than a second

summarize("chr1",0,240000000,5000) - less than a second

summarize("chr1",0,240000000,10000) - forever

Another property: when probed with many small querys at the resolution at which it gets stuck, it takes finite amount of time, but still slower compared to the resolution at which it doesn't get stuck.

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