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Bioconductor / GenomicRanges

Representation and manipulation of genomic intervals
https://bioconductor.org/packages/GenomicRanges
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Inefficiency of GPos("chr1:1-4e8") with GenomicRanges 1.37.7 #24

Closed hpages closed 5 years ago

hpages commented 5 years ago

Takes a long time and uses a lot of memory:

library(GenomicRanges)

system.time(gpos <- GPos("chr1:1-4e8"))
#    user  system elapsed 
#   7.342   3.723  11.070 

gc()
#           used (Mb) gc trigger   (Mb)   max used    (Mb)
# Ncells 2170379  116    4387842  234.4    2640964   141.1
# Vcells 3800652   29 1157310983 8829.6 1403787890 10710.1

gpos is stitched so construction should be very fast and use very little memory!

hpages commented 5 years ago

Fixed in GenomicRanges 1.37.8 (see commit cb3ece4433b09d8495f1af483904ede388fcbbfd)